Starting phenix.real_space_refine on Fri Jun 13 13:12:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tek_41189/06_2025/8tek_41189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tek_41189/06_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_41189/06_2025/8tek_41189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tek_41189/06_2025/8tek_41189.map" model { file = "/net/cci-nas-00/data/ceres_data/8tek_41189/06_2025/8tek_41189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tek_41189/06_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-5710/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: 9.90, per 1000 atoms: 0.65 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: 3.81 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: 1.37 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: 3.99 Time building geometry restraints manager: 4.51 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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.740 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.310 ------------------------------------------------------------------------------- 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 : 1.741 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: 0.3515 time to fit residues: 266.0772 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 : 1.870 ------------------------------------------------------------------------------- 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 = 68294.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.110626 restraints weight = 55199.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.110908 restraints weight = 47449.367| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 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 : 1.990 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: 0.7300 (mttt) cc_final: 0.6976 (mttt) REVERT: A 720 LYS cc_start: 0.5545 (tptt) cc_final: 0.5111 (tttt) REVERT: B 473 MET cc_start: -0.1094 (ttt) cc_final: -0.1411 (ttt) REVERT: E 300 HIS cc_start: 0.7047 (OUTLIER) cc_final: 0.6710 (t70) REVERT: E 342 LEU cc_start: 0.5318 (tp) cc_final: 0.5092 (tt) REVERT: E 401 GLN cc_start: 0.7715 (mt0) cc_final: 0.6700 (tp40) REVERT: M 236 MET cc_start: 0.7799 (ppp) cc_final: 0.7184 (mmm) REVERT: M 258 TYR cc_start: 0.3725 (p90) cc_final: 0.2101 (t80) REVERT: M 263 HIS cc_start: 0.7259 (m90) cc_final: 0.6921 (m90) REVERT: M 287 MET cc_start: 0.5569 (mmm) cc_final: 0.5134 (mmp) REVERT: N 692 ASN cc_start: 0.8390 (t0) cc_final: 0.8029 (t0) REVERT: N 695 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7462 (tttp) REVERT: O 586 TYR cc_start: 0.7252 (t80) cc_final: 0.6460 (m-80) outliers start: 43 outliers final: 24 residues processed: 306 average time/residue: 0.3440 time to fit residues: 144.2382 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 : 1.801 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 E 300 HIS ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 HIS P 666 ASN ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.127055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.107532 restraints weight = 68611.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.108726 restraints weight = 46325.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.108703 restraints weight = 30352.912| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.5244 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= 0.620 Angle : 0.703 16.525 20583 Z= 0.394 Chirality : 0.043 0.279 2269 Planarity : 0.005 0.075 2643 Dihedral : 5.081 42.636 1960 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 18.29 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z (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: -0.34 (0.19), residues: 1781 helix: 0.47 (0.14), residues: 1293 sheet: -0.55 (0.69), residues: 55 loop : -2.16 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 661 HIS 0.035 0.002 HIS B 289 PHE 0.021 0.002 PHE O 606 TYR 0.056 0.002 TYR A 295 ARG 0.008 0.001 ARG M 298 Details of bonding type rmsd hydrogen bonds : bond 0.06970 ( 1015) hydrogen bonds : angle 4.78641 ( 3021) covalent geometry : bond 0.01519 (15422) covalent geometry : angle 0.70279 (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 277 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 1.997 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 692 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7565 (p0) REVERT: A 720 LYS cc_start: 0.5907 (tptt) cc_final: 0.5663 (tppt) REVERT: B 318 MET cc_start: 0.6666 (ttp) cc_final: 0.6254 (tpp) REVERT: B 437 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: B 473 MET cc_start: -0.1200 (ttt) cc_final: -0.1499 (ttt) REVERT: D 380 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5213 (t) REVERT: D 442 HIS cc_start: 0.6361 (m-70) cc_final: 0.6090 (m170) REVERT: E 300 HIS cc_start: 0.6712 (OUTLIER) cc_final: 0.5265 (t-90) REVERT: E 307 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7441 (mp) REVERT: E 401 GLN cc_start: 0.7587 (mt0) cc_final: 0.6657 (tp40) REVERT: M 258 TYR cc_start: 0.3757 (p90) cc_final: 0.2176 (t80) REVERT: M 287 MET cc_start: 0.5472 (mmm) cc_final: 0.5083 (mmp) REVERT: N 670 MET cc_start: 0.7952 (mtp) cc_final: 0.7603 (mtm) REVERT: N 692 ASN cc_start: 0.8384 (t0) cc_final: 0.8022 (t0) REVERT: N 695 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7438 (tttp) REVERT: O 606 PHE cc_start: 0.5885 (t80) cc_final: 0.5389 (t80) REVERT: O 676 ARG cc_start: 0.7209 (tpt90) cc_final: 0.6649 (ttp-170) REVERT: P 696 ARG cc_start: 0.7142 (pmt-80) cc_final: 0.6861 (pmt-80) REVERT: T 247 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6227 (tt0) REVERT: T 294 LYS cc_start: 0.6669 (mmtt) cc_final: 0.6276 (mmtt) outliers start: 53 outliers final: 28 residues processed: 260 average time/residue: 0.3213 time to fit residues: 117.9856 Evaluate side-chains 221 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 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 437 LYS 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 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 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 672 ILE Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 290 GLU Chi-restraints excluded: chain g residue 89 PHE 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: 7.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN E 416 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** 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 710 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.125509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.109950 restraints weight = 68593.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109573 restraints weight = 53650.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.109578 restraints weight = 52303.801| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.061 15422 Z= 0.625 Angle : 0.705 16.612 20583 Z= 0.395 Chirality : 0.043 0.201 2269 Planarity : 0.005 0.077 2643 Dihedral : 5.137 43.874 1960 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 4.35 % Allowed : 20.29 % Favored : 75.35 % 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: -0.24 (0.20), residues: 1781 helix: 0.56 (0.14), residues: 1292 sheet: -0.63 (0.68), residues: 55 loop : -2.15 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 661 HIS 0.025 0.002 HIS E 300 PHE 0.022 0.002 PHE A 685 TYR 0.061 0.003 TYR A 295 ARG 0.010 0.001 ARG M 298 Details of bonding type rmsd hydrogen bonds : bond 0.06571 ( 1015) hydrogen bonds : angle 4.69679 ( 3021) covalent geometry : bond 0.01549 (15422) covalent geometry : angle 0.70521 (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 283 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 209 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7258 (mttp) cc_final: 0.6852 (pttt) REVERT: A 692 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 423 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: B 437 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8402 (mttp) REVERT: B 473 MET cc_start: -0.1600 (ttt) cc_final: -0.1914 (ttt) REVERT: D 380 VAL cc_start: 0.5754 (OUTLIER) cc_final: 0.5538 (t) REVERT: D 442 HIS cc_start: 0.6223 (m-70) cc_final: 0.5911 (m170) REVERT: E 300 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6013 (t70) REVERT: E 401 GLN cc_start: 0.7528 (mt0) cc_final: 0.6498 (tp40) REVERT: M 258 TYR cc_start: 0.4214 (p90) cc_final: 0.2342 (t80) REVERT: M 266 LEU cc_start: 0.2374 (OUTLIER) cc_final: 0.2097 (mm) REVERT: M 287 MET cc_start: 0.5600 (mmm) cc_final: 0.5225 (mmp) REVERT: N 568 ASP cc_start: 0.5483 (OUTLIER) cc_final: 0.4812 (m-30) REVERT: O 590 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: O 606 PHE cc_start: 0.5733 (t80) cc_final: 0.5259 (t80) REVERT: P 657 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7811 (mt-10) REVERT: P 684 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5831 (mp10) REVERT: T 247 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6179 (tt0) REVERT: T 294 LYS cc_start: 0.6799 (mmtt) cc_final: 0.6291 (mmtt) REVERT: T 301 GLU cc_start: 0.3443 (OUTLIER) cc_final: 0.3177 (mt-10) REVERT: g 90 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7433 (tt0) outliers start: 74 outliers final: 37 residues processed: 265 average time/residue: 0.3061 time to fit residues: 116.5342 Evaluate side-chains 230 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 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 416 ASN Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 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 P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 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 46 VAL 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 169 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** 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 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.109858 restraints weight = 69691.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.109728 restraints weight = 57094.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109812 restraints weight = 51036.519| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.008 15422 Z= 0.618 Angle : 0.704 16.924 20583 Z= 0.392 Chirality : 0.043 0.290 2269 Planarity : 0.005 0.077 2643 Dihedral : 5.104 44.264 1960 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 3.88 % Allowed : 21.76 % Favored : 74.35 % 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: -0.19 (0.20), residues: 1781 helix: 0.59 (0.14), residues: 1306 sheet: -0.66 (0.69), residues: 55 loop : -2.17 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 661 HIS 0.035 0.002 HIS B 289 PHE 0.021 0.002 PHE g 184 TYR 0.059 0.002 TYR A 295 ARG 0.007 0.001 ARG O 676 Details of bonding type rmsd hydrogen bonds : bond 0.06353 ( 1015) hydrogen bonds : angle 4.63463 ( 3021) covalent geometry : bond 0.01522 (15422) covalent geometry : angle 0.70357 (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 268 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7280 (mttp) cc_final: 0.6814 (pttm) REVERT: A 686 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7151 (tp30) REVERT: A 692 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (p0) REVERT: A 720 LYS cc_start: 0.5984 (tptt) cc_final: 0.5617 (tppt) REVERT: B 437 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8410 (mttp) REVERT: B 473 MET cc_start: -0.1112 (ttt) cc_final: -0.1426 (ttt) REVERT: D 442 HIS cc_start: 0.6372 (m-70) cc_final: 0.6145 (m170) REVERT: E 300 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.5783 (t70) REVERT: E 401 GLN cc_start: 0.7333 (mt0) cc_final: 0.6210 (tp40) REVERT: M 225 LYS cc_start: 0.7471 (tppt) cc_final: 0.6765 (tppt) REVERT: M 258 TYR cc_start: 0.4092 (p90) cc_final: 0.2351 (t80) REVERT: M 266 LEU cc_start: 0.2677 (OUTLIER) cc_final: 0.2270 (mm) REVERT: M 287 MET cc_start: 0.5678 (mmm) cc_final: 0.5273 (mmp) REVERT: M 324 HIS cc_start: 0.3209 (t-170) cc_final: 0.2452 (t-170) REVERT: N 568 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.4938 (m-30) REVERT: N 623 MET cc_start: 0.6859 (tpt) cc_final: 0.6594 (tpt) REVERT: O 586 TYR cc_start: 0.3144 (OUTLIER) cc_final: 0.1268 (t80) REVERT: O 590 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: O 606 PHE cc_start: 0.5791 (t80) cc_final: 0.5325 (t80) REVERT: T 247 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6227 (tt0) REVERT: T 294 LYS cc_start: 0.6853 (mmtt) cc_final: 0.6315 (mmtt) REVERT: T 301 GLU cc_start: 0.3466 (OUTLIER) cc_final: 0.3157 (mt-10) outliers start: 66 outliers final: 36 residues processed: 251 average time/residue: 0.3010 time to fit residues: 108.4440 Evaluate side-chains 228 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LYS 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 443 MET 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 E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 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 586 TYR 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 708 LEU Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 301 GLU 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 97 LYS Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 96 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS E 416 ASN ** M 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.123121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.108080 restraints weight = 68948.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.107591 restraints weight = 56505.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107772 restraints weight = 50712.579| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.043 15422 Z= 0.631 Angle : 0.764 17.207 20583 Z= 0.424 Chirality : 0.045 0.212 2269 Planarity : 0.005 0.087 2643 Dihedral : 5.350 45.892 1960 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 4.24 % Allowed : 23.06 % Favored : 72.71 % 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 (0.19), residues: 1781 helix: 0.42 (0.14), residues: 1320 sheet: -0.63 (0.75), residues: 48 loop : -2.31 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 661 HIS 0.022 0.002 HIS B 289 PHE 0.022 0.002 PHE A 685 TYR 0.062 0.003 TYR A 295 ARG 0.007 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06610 ( 1015) hydrogen bonds : angle 4.78663 ( 3021) covalent geometry : bond 0.01562 (15422) covalent geometry : angle 0.76443 (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 281 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7446 (mttp) cc_final: 0.6918 (pttm) REVERT: A 686 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7005 (tp30) REVERT: A 692 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7649 (p0) REVERT: A 728 MET cc_start: 0.7246 (pmm) cc_final: 0.6884 (pmm) REVERT: B 319 GLN cc_start: 0.7356 (mm110) cc_final: 0.7139 (mm110) REVERT: B 473 MET cc_start: -0.1199 (ttt) cc_final: -0.1404 (ttt) REVERT: E 264 LYS cc_start: 0.7227 (tttt) cc_final: 0.6801 (mmmt) REVERT: E 300 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6323 (t70) REVERT: E 371 LEU cc_start: 0.6164 (mp) cc_final: 0.5953 (mt) REVERT: E 401 GLN cc_start: 0.7633 (mt0) cc_final: 0.6316 (tp40) REVERT: M 225 LYS cc_start: 0.7582 (tppt) cc_final: 0.6743 (tppt) REVERT: M 258 TYR cc_start: 0.4188 (p90) cc_final: 0.2558 (t80) REVERT: M 287 MET cc_start: 0.4980 (mmm) cc_final: 0.4704 (mmp) REVERT: N 568 ASP cc_start: 0.5225 (OUTLIER) cc_final: 0.4659 (m-30) REVERT: O 590 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: O 681 MET cc_start: 0.5506 (tpt) cc_final: 0.5189 (ttp) REVERT: P 684 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: P 696 ARG cc_start: 0.6939 (pmt-80) cc_final: 0.6631 (pmt-80) REVERT: T 294 LYS cc_start: 0.6877 (mmtt) cc_final: 0.6342 (mmtt) REVERT: T 296 TYR cc_start: 0.7063 (m-10) cc_final: 0.6823 (m-10) REVERT: T 301 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.4319 (mp0) REVERT: T 343 LEU cc_start: 0.7256 (mp) cc_final: 0.6664 (mp) outliers start: 72 outliers final: 46 residues processed: 265 average time/residue: 0.3042 time to fit residues: 116.5153 Evaluate side-chains 236 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 293 PHE 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 313 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 416 ASN 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 236 MET Chi-restraints excluded: chain M residue 249 ASP 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 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 759 ASP 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 97 LYS Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 30.0000 chunk 174 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 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** M 289 GLN M 332 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.109188 restraints weight = 69610.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.109639 restraints weight = 52767.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109644 restraints weight = 49321.089| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.067 15422 Z= 0.615 Angle : 0.692 16.555 20583 Z= 0.387 Chirality : 0.043 0.246 2269 Planarity : 0.004 0.079 2643 Dihedral : 5.038 44.880 1960 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Rotamer: Outliers : 4.00 % Allowed : 24.53 % Favored : 71.47 % 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: -0.10 (0.20), residues: 1781 helix: 0.65 (0.14), residues: 1325 sheet: -0.53 (0.76), residues: 48 loop : -2.26 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 661 HIS 0.022 0.002 HIS B 289 PHE 0.022 0.002 PHE O 606 TYR 0.059 0.002 TYR A 295 ARG 0.007 0.000 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06080 ( 1015) hydrogen bonds : angle 4.55766 ( 3021) covalent geometry : bond 0.01528 (15422) covalent geometry : angle 0.69153 (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 276 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 1.848 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 339 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: A 686 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: A 692 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7650 (p0) REVERT: A 720 LYS cc_start: 0.5559 (tptt) cc_final: 0.5166 (tppt) REVERT: A 728 MET cc_start: 0.7290 (pmm) cc_final: 0.6920 (pmm) REVERT: B 319 GLN cc_start: 0.7167 (mm110) cc_final: 0.6894 (mm110) REVERT: B 473 MET cc_start: -0.1260 (ttt) cc_final: -0.1539 (ttt) REVERT: E 264 LYS cc_start: 0.7184 (tttt) cc_final: 0.6747 (mmmt) REVERT: E 300 HIS cc_start: 0.6869 (OUTLIER) cc_final: 0.5867 (t70) REVERT: E 401 GLN cc_start: 0.7252 (mt0) cc_final: 0.6142 (tp40) REVERT: M 225 LYS cc_start: 0.7386 (tppt) cc_final: 0.6686 (tppt) REVERT: M 258 TYR cc_start: 0.4326 (p90) cc_final: 0.2777 (t80) REVERT: N 568 ASP cc_start: 0.5550 (OUTLIER) cc_final: 0.4988 (m-30) REVERT: O 525 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: O 590 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: O 606 PHE cc_start: 0.5730 (t80) cc_final: 0.5118 (t80) REVERT: O 681 MET cc_start: 0.5360 (tpt) cc_final: 0.5108 (ttp) REVERT: T 247 GLU cc_start: 0.6861 (tm-30) cc_final: 0.6304 (tt0) REVERT: T 294 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6572 (mmtt) REVERT: T 301 GLU cc_start: 0.4618 (OUTLIER) cc_final: 0.4187 (mp0) REVERT: g 124 ARG cc_start: 0.6825 (tpp-160) cc_final: 0.6399 (mmt-90) outliers start: 68 outliers final: 38 residues processed: 259 average time/residue: 0.3017 time to fit residues: 111.5907 Evaluate side-chains 235 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN 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 442 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 314 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 219 ILE Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 285 TYR 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 632 GLU 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 644 GLN 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 704 MET Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain g residue 138 ASP Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 406 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN M 289 GLN ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.122435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.108186 restraints weight = 69621.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.107548 restraints weight = 66470.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.107944 restraints weight = 56580.031| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.076 15422 Z= 0.629 Angle : 0.769 16.540 20583 Z= 0.422 Chirality : 0.045 0.226 2269 Planarity : 0.005 0.087 2643 Dihedral : 5.307 45.884 1960 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 4.29 % Allowed : 24.00 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.20), residues: 1781 helix: 0.54 (0.14), residues: 1319 sheet: -0.64 (0.75), residues: 48 loop : -2.23 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 661 HIS 0.020 0.002 HIS B 289 PHE 0.024 0.002 PHE O 606 TYR 0.058 0.003 TYR A 295 ARG 0.009 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06401 ( 1015) hydrogen bonds : angle 4.73046 ( 3021) covalent geometry : bond 0.01566 (15422) covalent geometry : angle 0.76867 (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 264 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 TRP cc_start: 0.5065 (m-90) cc_final: 0.4844 (m100) REVERT: A 686 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 688 GLN cc_start: 0.6917 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 728 MET cc_start: 0.7239 (pmm) cc_final: 0.6919 (pmm) REVERT: B 267 ARG cc_start: 0.7333 (ttt180) cc_final: 0.7132 (ttt-90) REVERT: B 319 GLN cc_start: 0.7363 (mm110) cc_final: 0.7127 (mm110) REVERT: B 473 MET cc_start: -0.0918 (ttt) cc_final: -0.1145 (ttt) REVERT: D 442 HIS cc_start: 0.6360 (m170) cc_final: 0.6122 (m170) REVERT: E 264 LYS cc_start: 0.7206 (tttt) cc_final: 0.6803 (mmmt) REVERT: E 300 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6009 (t70) REVERT: E 401 GLN cc_start: 0.7573 (mt0) cc_final: 0.5933 (tp40) REVERT: M 225 LYS cc_start: 0.7469 (tppt) cc_final: 0.6671 (tppt) REVERT: M 258 TYR cc_start: 0.4328 (p90) cc_final: 0.2980 (t80) REVERT: M 345 GLN cc_start: 0.4126 (OUTLIER) cc_final: 0.3892 (pm20) REVERT: N 568 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.4872 (m-30) REVERT: O 525 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: O 590 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: O 606 PHE cc_start: 0.5403 (t80) cc_final: 0.4853 (t80) REVERT: P 684 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5953 (mp10) REVERT: T 247 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6163 (tt0) REVERT: T 294 LYS cc_start: 0.6832 (mmtt) cc_final: 0.6274 (mmtt) REVERT: T 301 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4694 (mp0) REVERT: g 124 ARG cc_start: 0.6711 (tpp-160) cc_final: 0.6326 (mmt-90) outliers start: 73 outliers final: 44 residues processed: 248 average time/residue: 0.2892 time to fit residues: 103.7979 Evaluate side-chains 234 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 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 E residue 300 HIS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 416 ASN 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 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain M residue 345 GLN Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 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 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 138 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 13 optimal weight: 0.0370 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- 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 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 568 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.124029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.109007 restraints weight = 69129.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109582 restraints weight = 54283.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.109593 restraints weight = 48820.786| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.7280 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= 0.617 Angle : 0.729 16.487 20583 Z= 0.403 Chirality : 0.044 0.276 2269 Planarity : 0.004 0.079 2643 Dihedral : 5.111 45.334 1960 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 3.18 % Allowed : 25.59 % 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: -0.07 (0.20), residues: 1781 helix: 0.69 (0.14), residues: 1321 sheet: -0.66 (0.76), residues: 48 loop : -2.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 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 0.010 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06021 ( 1015) hydrogen bonds : angle 4.59514 ( 3021) covalent geometry : bond 0.01540 (15422) covalent geometry : angle 0.72925 (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 255 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 682 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8253 (mmmm) REVERT: A 686 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6956 (tp30) REVERT: A 688 GLN cc_start: 0.6821 (tm-30) cc_final: 0.6587 (tm-30) REVERT: A 720 LYS cc_start: 0.5591 (tptt) cc_final: 0.5236 (tppt) REVERT: A 728 MET cc_start: 0.7545 (pmm) cc_final: 0.7176 (pmm) REVERT: B 319 GLN cc_start: 0.7168 (mm110) cc_final: 0.6906 (mm110) REVERT: E 264 LYS cc_start: 0.7150 (tttt) cc_final: 0.6751 (mmmt) REVERT: E 300 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5911 (t70) REVERT: E 401 GLN cc_start: 0.7154 (mt0) cc_final: 0.6746 (mt0) REVERT: M 225 LYS cc_start: 0.7470 (tppt) cc_final: 0.6700 (tppt) REVERT: M 258 TYR cc_start: 0.4178 (p90) cc_final: 0.2815 (t80) REVERT: M 345 GLN cc_start: 0.4089 (OUTLIER) cc_final: 0.3841 (pm20) REVERT: N 568 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5001 (m-30) REVERT: N 728 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7598 (mp) REVERT: O 525 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: O 590 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: O 606 PHE cc_start: 0.5729 (t80) cc_final: 0.5162 (t80) REVERT: P 684 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5967 (mp10) REVERT: T 247 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6266 (tt0) REVERT: T 280 LYS cc_start: 0.7168 (mmtm) cc_final: 0.6930 (mmtm) REVERT: T 294 LYS cc_start: 0.6729 (mmtt) cc_final: 0.6454 (mmtt) REVERT: T 301 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4609 (mp0) REVERT: g 124 ARG cc_start: 0.6828 (tpp-160) cc_final: 0.6435 (mmt-90) outliers start: 54 outliers final: 34 residues processed: 242 average time/residue: 0.3153 time to fit residues: 109.3164 Evaluate side-chains 226 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 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 442 GLN Chi-restraints excluded: chain E residue 300 HIS 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 219 ILE Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain M residue 345 GLN Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 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 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 704 MET Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.123551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.109135 restraints weight = 69977.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.109633 restraints weight = 63992.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.109708 restraints weight = 50975.354| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.086 15422 Z= 0.620 Angle : 0.745 16.485 20583 Z= 0.412 Chirality : 0.044 0.249 2269 Planarity : 0.005 0.083 2643 Dihedral : 5.126 44.926 1960 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 2.82 % Allowed : 26.18 % Favored : 71.00 % 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: -0.09 (0.20), residues: 1781 helix: 0.67 (0.14), residues: 1315 sheet: -0.58 (0.82), residues: 43 loop : -2.19 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 661 HIS 0.020 0.002 HIS B 289 PHE 0.024 0.002 PHE M 300 TYR 0.056 0.002 TYR A 295 ARG 0.012 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06053 ( 1015) hydrogen bonds : angle 4.61934 ( 3021) covalent geometry : bond 0.01549 (15422) covalent geometry : angle 0.74508 (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 231 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6997 (tp30) REVERT: A 728 MET cc_start: 0.7481 (pmm) cc_final: 0.7209 (pmm) REVERT: B 319 GLN cc_start: 0.7450 (mm110) cc_final: 0.7224 (mm110) REVERT: E 264 LYS cc_start: 0.7133 (tttt) cc_final: 0.6742 (mmmt) REVERT: E 300 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6013 (t70) REVERT: E 401 GLN cc_start: 0.7202 (mt0) cc_final: 0.6993 (mt0) REVERT: M 225 LYS cc_start: 0.7433 (tppt) cc_final: 0.6695 (tppt) REVERT: M 248 GLU cc_start: 0.6797 (tp30) cc_final: 0.6047 (tm-30) REVERT: M 258 TYR cc_start: 0.3767 (p90) cc_final: 0.2530 (t80) REVERT: N 568 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.4951 (m-30) REVERT: N 728 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7656 (mp) REVERT: O 525 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: O 590 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: O 606 PHE cc_start: 0.5669 (t80) cc_final: 0.5157 (t80) REVERT: P 684 GLN cc_start: 0.6420 (OUTLIER) cc_final: 0.5955 (mp10) REVERT: T 247 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6341 (tt0) REVERT: T 280 LYS cc_start: 0.7131 (mmtm) cc_final: 0.6908 (mmtm) REVERT: T 294 LYS cc_start: 0.6763 (mmtt) cc_final: 0.6490 (mmtt) REVERT: T 301 GLU cc_start: 0.4954 (OUTLIER) cc_final: 0.4606 (mp0) REVERT: g 124 ARG cc_start: 0.6857 (tpp-160) cc_final: 0.6470 (mmt-90) outliers start: 48 outliers final: 36 residues processed: 220 average time/residue: 0.3080 time to fit residues: 98.6485 Evaluate side-chains 221 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 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 442 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 456 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 219 ILE Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE 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 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 P residue 704 MET Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE 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: 5.9990 chunk 113 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.122267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.107778 restraints weight = 69106.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.107182 restraints weight = 60085.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.107589 restraints weight = 51909.675| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.087 15422 Z= 0.625 Angle : 0.772 16.478 20583 Z= 0.426 Chirality : 0.045 0.225 2269 Planarity : 0.005 0.082 2643 Dihedral : 5.205 45.927 1960 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 2.94 % Allowed : 26.53 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.20), residues: 1781 helix: 0.60 (0.14), residues: 1312 sheet: -0.74 (0.82), residues: 43 loop : -2.14 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 700 HIS 0.020 0.002 HIS B 289 PHE 0.023 0.002 PHE M 300 TYR 0.055 0.002 TYR A 295 ARG 0.011 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06180 ( 1015) hydrogen bonds : angle 4.69088 ( 3021) covalent geometry : bond 0.01562 (15422) covalent geometry : angle 0.77220 (20583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7343.14 seconds wall clock time: 127 minutes 12.64 seconds (7632.64 seconds total)