Starting phenix.real_space_refine on Wed Mar 4 22:39:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpr_22420/03_2026/7jpr_22420.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 10721 2.51 5 N 2838 2.21 5 O 3082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16737 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4858 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 24, 'TRANS': 568} Chain breaks: 8 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3168 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 369} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.22 Number of scatterers: 16737 At special positions: 0 Unit cell: (102.72, 131.61, 175.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 9 15.00 Mg 3 11.99 O 3082 8.00 N 2838 7.00 C 10721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 803.4 milliseconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 8 sheets defined 63.0% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.841A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 removed outlier: 3.546A pdb=" N ALA A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 removed outlier: 4.322A pdb=" N VAL A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.818A pdb=" N TRP A 626 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.619A pdb=" N MET A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.525A pdb=" N LEU A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.925A pdb=" N ILE A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 736 Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.797A pdb=" N SER A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.640A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.695A pdb=" N CYS A 829 " --> pdb=" O HIS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 860 removed outlier: 3.582A pdb=" N VAL A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 284 through 297 removed outlier: 3.568A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.820A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.712A pdb=" N ARG B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.141A pdb=" N LEU B 431 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET B 432 " --> pdb=" O ALA B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 432' Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.058A pdb=" N SER B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 Processing helix chain 'B' and resid 512 through 523 removed outlier: 3.595A pdb=" N ALA B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.929A pdb=" N HIS B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 36 through 86 removed outlier: 3.512A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.500A pdb=" N GLU C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.597A pdb=" N ILE C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.564A pdb=" N TRP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.561A pdb=" N PHE C 225 " --> pdb=" O MET C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.682A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 257 through 263 removed outlier: 3.574A pdb=" N ARG C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.504A pdb=" N ILE C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 330 " --> pdb=" O LYS C 326 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 333 " --> pdb=" O GLN C 329 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 3.890A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.899A pdb=" N ARG C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.535A pdb=" N ARG C 374 " --> pdb=" O PRO C 370 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.595A pdb=" N LEU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.634A pdb=" N THR C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 removed outlier: 3.541A pdb=" N CYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.885A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 3.531A pdb=" N LYS C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.980A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.642A pdb=" N GLU C 554 " --> pdb=" O GLU C 550 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 592 removed outlier: 3.779A pdb=" N LEU C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.616A pdb=" N HIS C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 638 removed outlier: 3.586A pdb=" N ALA C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 634 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 637 " --> pdb=" O ALA C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 removed outlier: 3.636A pdb=" N VAL C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 691 removed outlier: 3.674A pdb=" N ARG C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 86 Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.547A pdb=" N ASN D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.601A pdb=" N LEU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.640A pdb=" N LEU D 163 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 removed outlier: 4.110A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.983A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.533A pdb=" N ALA D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.745A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.916A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.549A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.587A pdb=" N ASN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.723A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.776A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.633A pdb=" N ARG D 426 " --> pdb=" O PRO D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 42 through 54 removed outlier: 4.019A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 126 through 130 removed outlier: 3.811A pdb=" N TYR E 129 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 removed outlier: 3.569A pdb=" N ARG E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.515A pdb=" N TYR E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.517A pdb=" N LEU E 225 " --> pdb=" O ASP E 221 " (cutoff:3.500A) Proline residue: E 234 - end of helix removed outlier: 3.547A pdb=" N CYS E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 249 through 268 Proline residue: E 259 - end of helix removed outlier: 4.404A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.740A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 329' Processing helix chain 'E' and resid 358 through 370 removed outlier: 4.026A pdb=" N SER E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 388 removed outlier: 4.057A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 387 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 4.028A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 419 " --> pdb=" O PHE E 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 4.239A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.864A pdb=" N THR A 674 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 832 through 833 removed outlier: 3.501A pdb=" N ARG A 846 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 339 removed outlier: 3.522A pdb=" N PHE B 389 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 423 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 312 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR B 446 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 314 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 136 removed outlier: 3.725A pdb=" N ILE C 252 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 95 through 100 removed outlier: 6.553A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG D 213 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 64 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 215 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.618A pdb=" N VAL E 59 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP E 125 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL E 61 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 393 through 395 804 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4031 1.33 - 1.45: 3456 1.45 - 1.58: 9449 1.58 - 1.70: 15 1.70 - 1.82: 127 Bond restraints: 17078 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.75e+01 ... (remaining 17073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 22831 4.43 - 8.87: 258 8.87 - 13.30: 22 13.30 - 17.73: 3 17.73 - 22.16: 3 Bond angle restraints: 23117 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.71 22.16 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 120.25 19.62 1.00e+00 1.00e+00 3.85e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 119.68 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 121.58 15.25 1.00e+00 1.00e+00 2.33e+02 ... (remaining 23112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9291 17.95 - 35.90: 885 35.90 - 53.86: 161 53.86 - 71.81: 42 71.81 - 89.76: 28 Dihedral angle restraints: 10407 sinusoidal: 4338 harmonic: 6069 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP A 631 " pdb=" C ASP A 631 " pdb=" N ILE A 632 " pdb=" CA ILE A 632 " ideal model delta harmonic sigma weight residual 180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR D 339 " pdb=" C TYR D 339 " pdb=" N GLU D 340 " pdb=" CA GLU D 340 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 10404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2182 0.079 - 0.158: 401 0.158 - 0.237: 44 0.237 - 0.316: 11 0.316 - 0.396: 3 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CB THR B 448 " pdb=" CA THR B 448 " pdb=" OG1 THR B 448 " pdb=" CG2 THR B 448 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU B 444 " pdb=" CB LEU B 444 " pdb=" CD1 LEU B 444 " pdb=" CD2 LEU B 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2638 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 404 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO E 405 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO E 405 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 405 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 49 " 0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CD GLU D 49 " -0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU D 49 " 0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU D 49 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 84 " 0.015 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE C 84 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 84 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE C 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 84 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 84 " 0.001 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 123 2.62 - 3.19: 13804 3.19 - 3.76: 25762 3.76 - 4.33: 33808 4.33 - 4.90: 54414 Nonbonded interactions: 127911 Sorted by model distance: nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.048 2.170 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.114 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.147 2.170 nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.149 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.155 2.170 ... (remaining 127906 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: 3.070 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.970 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 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 : 0.006 0.080 17078 Z= 0.387 Angle : 1.201 22.163 23117 Z= 0.719 Chirality : 0.062 0.396 2641 Planarity : 0.007 0.124 2912 Dihedral : 15.309 89.759 6435 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.16), residues: 2005 helix: -1.82 (0.12), residues: 1160 sheet: 0.44 (0.39), residues: 166 loop : -2.10 (0.20), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 150 TYR 0.039 0.003 TYR C 408 PHE 0.056 0.004 PHE D 245 TRP 0.046 0.004 TRP A 639 HIS 0.021 0.002 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00646 (17078) covalent geometry : angle 1.20146 (23117) hydrogen bonds : bond 0.22981 ( 804) hydrogen bonds : angle 7.11731 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASN cc_start: 0.9413 (m-40) cc_final: 0.9144 (p0) REVERT: A 633 MET cc_start: 0.8281 (pmm) cc_final: 0.7978 (pmm) REVERT: A 852 ASP cc_start: 0.8530 (m-30) cc_final: 0.8002 (p0) REVERT: C 321 VAL cc_start: 0.9074 (m) cc_final: 0.8649 (t) REVERT: C 414 LEU cc_start: 0.9118 (mp) cc_final: 0.8850 (mp) REVERT: C 422 PHE cc_start: 0.7956 (m-80) cc_final: 0.7753 (m-80) REVERT: C 423 THR cc_start: 0.8482 (m) cc_final: 0.8281 (p) REVERT: D 174 TYR cc_start: 0.7652 (t80) cc_final: 0.7018 (t80) REVERT: D 281 MET cc_start: 0.7777 (tmm) cc_final: 0.7560 (tmm) REVERT: D 314 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8015 (mttt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1283 time to fit residues: 53.3633 Evaluate side-chains 157 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 GLN B 411 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 254 GLN D 358 GLN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.064538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.047405 restraints weight = 136798.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048330 restraints weight = 96673.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.049054 restraints weight = 75886.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.049511 restraints weight = 63613.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.049782 restraints weight = 56375.675| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17078 Z= 0.141 Angle : 0.675 11.634 23117 Z= 0.340 Chirality : 0.041 0.168 2641 Planarity : 0.005 0.075 2912 Dihedral : 7.778 88.068 2296 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.49 % Allowed : 8.37 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.17), residues: 2005 helix: -0.18 (0.14), residues: 1180 sheet: 0.60 (0.39), residues: 165 loop : -1.49 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 205 TYR 0.022 0.002 TYR C 337 PHE 0.024 0.001 PHE C 693 TRP 0.016 0.002 TRP A 639 HIS 0.005 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00297 (17078) covalent geometry : angle 0.67539 (23117) hydrogen bonds : bond 0.04645 ( 804) hydrogen bonds : angle 4.44894 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 ASN cc_start: 0.9779 (m-40) cc_final: 0.9459 (p0) REVERT: A 633 MET cc_start: 0.8785 (pmm) cc_final: 0.8484 (pmm) REVERT: A 852 ASP cc_start: 0.9210 (m-30) cc_final: 0.8647 (p0) REVERT: B 432 MET cc_start: 0.7891 (ptp) cc_final: 0.7387 (pmm) REVERT: C 29 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: C 140 ASP cc_start: 0.9229 (p0) cc_final: 0.8996 (p0) REVERT: C 189 MET cc_start: 0.8273 (mmt) cc_final: 0.8030 (mmt) REVERT: C 321 VAL cc_start: 0.8896 (m) cc_final: 0.8426 (t) REVERT: C 422 PHE cc_start: 0.8505 (m-80) cc_final: 0.8266 (m-80) REVERT: C 469 MET cc_start: 0.7869 (ppp) cc_final: 0.7668 (ppp) REVERT: C 482 TYR cc_start: 0.7946 (t80) cc_final: 0.7435 (t80) REVERT: C 634 TYR cc_start: 0.8079 (t80) cc_final: 0.7822 (t80) REVERT: C 673 MET cc_start: 0.5249 (pmm) cc_final: 0.3617 (ppp) REVERT: C 691 LEU cc_start: 0.8890 (tt) cc_final: 0.8681 (tt) REVERT: D 75 MET cc_start: 0.8613 (ttp) cc_final: 0.8346 (ptm) REVERT: D 303 MET cc_start: 0.9094 (mtp) cc_final: 0.8809 (ptp) REVERT: D 388 MET cc_start: 0.6676 (ptp) cc_final: 0.6326 (mtt) REVERT: D 412 MET cc_start: 0.8988 (ptp) cc_final: 0.8725 (tmm) REVERT: E 265 MET cc_start: 0.8677 (ptt) cc_final: 0.8259 (tmm) outliers start: 28 outliers final: 19 residues processed: 186 average time/residue: 0.1175 time to fit residues: 34.3825 Evaluate side-chains 162 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 194 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN C 365 ASN ** C 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 106 ASN D 216 HIS D 358 GLN D 410 GLN D 427 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.064059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.047814 restraints weight = 147670.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.048716 restraints weight = 103000.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.049402 restraints weight = 80368.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.049737 restraints weight = 67236.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.050098 restraints weight = 60047.333| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17078 Z= 0.116 Angle : 0.606 13.838 23117 Z= 0.299 Chirality : 0.040 0.162 2641 Planarity : 0.004 0.054 2912 Dihedral : 7.151 79.089 2296 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.65 % Allowed : 10.77 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2005 helix: 0.60 (0.15), residues: 1183 sheet: 0.63 (0.39), residues: 173 loop : -1.31 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 844 TYR 0.016 0.001 TYR C 610 PHE 0.019 0.001 PHE C 479 TRP 0.014 0.001 TRP B 445 HIS 0.004 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00250 (17078) covalent geometry : angle 0.60631 (23117) hydrogen bonds : bond 0.03713 ( 804) hydrogen bonds : angle 4.04522 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.691 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 633 MET cc_start: 0.8925 (pmm) cc_final: 0.8550 (pmm) REVERT: A 852 ASP cc_start: 0.9255 (m-30) cc_final: 0.8762 (p0) REVERT: B 432 MET cc_start: 0.7986 (ptp) cc_final: 0.7528 (pmm) REVERT: C 189 MET cc_start: 0.8201 (mmt) cc_final: 0.7951 (mmt) REVERT: C 321 VAL cc_start: 0.8985 (m) cc_final: 0.8631 (t) REVERT: C 422 PHE cc_start: 0.8544 (m-80) cc_final: 0.8306 (m-80) REVERT: C 469 MET cc_start: 0.8059 (ppp) cc_final: 0.7824 (ppp) REVERT: C 482 TYR cc_start: 0.8111 (t80) cc_final: 0.7275 (t80) REVERT: C 634 TYR cc_start: 0.7972 (t80) cc_final: 0.7542 (t80) REVERT: C 693 PHE cc_start: 0.8410 (m-80) cc_final: 0.7977 (m-80) REVERT: D 51 LEU cc_start: 0.9785 (mt) cc_final: 0.9349 (pp) REVERT: D 75 MET cc_start: 0.8751 (ttp) cc_final: 0.8482 (ptm) REVERT: D 249 TRP cc_start: 0.8848 (t-100) cc_final: 0.8462 (t-100) REVERT: D 281 MET cc_start: 0.7538 (tmm) cc_final: 0.7313 (tmm) REVERT: D 373 MET cc_start: 0.8582 (tmm) cc_final: 0.8253 (ptt) REVERT: D 388 MET cc_start: 0.6461 (ptp) cc_final: 0.6034 (mtt) REVERT: D 402 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8754 (mmp) REVERT: E 265 MET cc_start: 0.8639 (ptt) cc_final: 0.8199 (tmm) outliers start: 31 outliers final: 24 residues processed: 170 average time/residue: 0.1205 time to fit residues: 32.1307 Evaluate side-chains 155 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 44 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS A 596 HIS A 825 HIS B 306 HIS B 310 ASN B 362 HIS ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 519 GLN C 53 GLN C 146 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN C 365 ASN ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 HIS D 263 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 378 HIS D 394 ASN E 256 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN E 383 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.054659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.039731 restraints weight = 146372.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.040412 restraints weight = 109329.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.040901 restraints weight = 89875.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.041131 restraints weight = 78465.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.041347 restraints weight = 72305.922| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 17078 Z= 0.378 Angle : 0.967 14.358 23117 Z= 0.495 Chirality : 0.051 0.198 2641 Planarity : 0.006 0.065 2912 Dihedral : 8.819 86.634 2296 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.36 % Allowed : 13.70 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2005 helix: -0.71 (0.14), residues: 1205 sheet: 0.23 (0.38), residues: 169 loop : -1.64 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 546 TYR 0.028 0.003 TYR C 610 PHE 0.033 0.003 PHE B 343 TRP 0.035 0.003 TRP B 445 HIS 0.012 0.002 HIS E 260 Details of bonding type rmsd covalent geometry : bond 0.00790 (17078) covalent geometry : angle 0.96675 (23117) hydrogen bonds : bond 0.05529 ( 804) hydrogen bonds : angle 5.27071 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8107 (ttp80) REVERT: B 433 TRP cc_start: 0.8695 (p90) cc_final: 0.8416 (p90) REVERT: C 29 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: C 178 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7690 (t70) REVERT: C 260 HIS cc_start: 0.8445 (t-170) cc_final: 0.8093 (t-170) REVERT: C 362 GLN cc_start: 0.5461 (OUTLIER) cc_final: 0.4817 (mm110) REVERT: C 365 ASN cc_start: 0.9035 (t0) cc_final: 0.8642 (m-40) REVERT: C 394 LEU cc_start: 0.8999 (tp) cc_final: 0.8664 (mt) REVERT: C 617 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8937 (pptt) REVERT: C 673 MET cc_start: 0.6575 (pmm) cc_final: 0.6369 (pmm) REVERT: D 64 LEU cc_start: 0.9559 (mt) cc_final: 0.9340 (tt) REVERT: E 93 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (tp30) outliers start: 63 outliers final: 41 residues processed: 182 average time/residue: 0.1165 time to fit residues: 33.5247 Evaluate side-chains 167 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 844 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 362 GLN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 617 LYS Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 263 LYS Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 200 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 347 GLN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.057679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.042021 restraints weight = 141241.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.042723 restraints weight = 101636.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.043317 restraints weight = 82006.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.043705 restraints weight = 70869.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.043965 restraints weight = 63939.461| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17078 Z= 0.131 Angle : 0.664 13.004 23117 Z= 0.324 Chirality : 0.041 0.173 2641 Planarity : 0.004 0.052 2912 Dihedral : 7.615 78.859 2296 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 15.99 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 2005 helix: 0.27 (0.15), residues: 1196 sheet: 0.35 (0.39), residues: 174 loop : -1.33 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.015 0.001 TYR C 610 PHE 0.019 0.001 PHE C 479 TRP 0.025 0.002 TRP B 445 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00285 (17078) covalent geometry : angle 0.66419 (23117) hydrogen bonds : bond 0.03887 ( 804) hydrogen bonds : angle 4.36471 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 633 MET cc_start: 0.9231 (pmm) cc_final: 0.8902 (pmm) REVERT: A 816 MET cc_start: 0.8293 (ptp) cc_final: 0.6900 (ptp) REVERT: B 287 LEU cc_start: 0.9527 (mm) cc_final: 0.9199 (pp) REVERT: B 432 MET cc_start: 0.8153 (ptp) cc_final: 0.7659 (ptp) REVERT: B 433 TRP cc_start: 0.8560 (p90) cc_final: 0.8090 (p90) REVERT: C 29 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: C 178 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7614 (t70) REVERT: C 181 MET cc_start: 0.6555 (ttp) cc_final: 0.6240 (tmm) REVERT: C 189 MET cc_start: 0.8327 (mmt) cc_final: 0.8104 (mmt) REVERT: C 365 ASN cc_start: 0.8826 (t0) cc_final: 0.8478 (m-40) REVERT: C 394 LEU cc_start: 0.8934 (tp) cc_final: 0.8612 (mt) REVERT: C 469 MET cc_start: 0.8770 (tmm) cc_final: 0.8024 (ppp) REVERT: D 51 LEU cc_start: 0.9797 (mt) cc_final: 0.9363 (pp) REVERT: D 64 LEU cc_start: 0.9569 (mt) cc_final: 0.9351 (tt) REVERT: D 75 MET cc_start: 0.8861 (ttp) cc_final: 0.8507 (ptm) REVERT: D 314 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8006 (mtmt) REVERT: D 373 MET cc_start: 0.8719 (tmm) cc_final: 0.8312 (ptt) REVERT: E 133 MET cc_start: 0.8595 (ttm) cc_final: 0.7534 (mmm) REVERT: E 406 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9134 (mtmm) outliers start: 44 outliers final: 25 residues processed: 174 average time/residue: 0.1116 time to fit residues: 31.0722 Evaluate side-chains 152 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 63 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.058587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.043325 restraints weight = 154511.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.044130 restraints weight = 107202.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.044746 restraints weight = 84351.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.045088 restraints weight = 70967.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.045410 restraints weight = 63649.790| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17078 Z= 0.117 Angle : 0.629 12.274 23117 Z= 0.305 Chirality : 0.041 0.332 2641 Planarity : 0.004 0.053 2912 Dihedral : 7.287 77.624 2296 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 16.68 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 2005 helix: 0.70 (0.15), residues: 1195 sheet: 0.57 (0.40), residues: 174 loop : -1.19 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 546 TYR 0.013 0.001 TYR D 399 PHE 0.035 0.001 PHE D 353 TRP 0.018 0.001 TRP B 445 HIS 0.010 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00259 (17078) covalent geometry : angle 0.62866 (23117) hydrogen bonds : bond 0.03469 ( 804) hydrogen bonds : angle 4.13416 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 633 MET cc_start: 0.9233 (pmm) cc_final: 0.8973 (pmm) REVERT: A 816 MET cc_start: 0.8150 (ptp) cc_final: 0.7511 (ptp) REVERT: A 820 MET cc_start: 0.9213 (mtt) cc_final: 0.9004 (ptp) REVERT: A 852 ASP cc_start: 0.9230 (m-30) cc_final: 0.8743 (p0) REVERT: B 287 LEU cc_start: 0.9530 (mm) cc_final: 0.9197 (pp) REVERT: B 302 MET cc_start: 0.4293 (tpt) cc_final: 0.3415 (tmm) REVERT: B 409 ILE cc_start: 0.9197 (mm) cc_final: 0.8923 (pt) REVERT: B 432 MET cc_start: 0.8164 (ptp) cc_final: 0.7649 (ptp) REVERT: B 433 TRP cc_start: 0.8553 (p90) cc_final: 0.8069 (p90) REVERT: C 29 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: C 189 MET cc_start: 0.8291 (mmt) cc_final: 0.8004 (mmt) REVERT: C 365 ASN cc_start: 0.8787 (t0) cc_final: 0.8464 (m-40) REVERT: C 394 LEU cc_start: 0.8943 (tp) cc_final: 0.8621 (mt) REVERT: D 64 LEU cc_start: 0.9548 (mt) cc_final: 0.9333 (tt) REVERT: D 75 MET cc_start: 0.8856 (ttp) cc_final: 0.8576 (ptm) REVERT: D 314 LYS cc_start: 0.8773 (mmtp) cc_final: 0.7975 (mtmt) REVERT: D 373 MET cc_start: 0.8808 (tmm) cc_final: 0.8378 (ptt) REVERT: D 388 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6098 (mpp) outliers start: 41 outliers final: 27 residues processed: 170 average time/residue: 0.1060 time to fit residues: 29.1446 Evaluate side-chains 159 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 64 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 398 HIS ** 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 = 0.3675 r_free = 0.3675 target = 0.056461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.041150 restraints weight = 142829.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.041821 restraints weight = 104622.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042315 restraints weight = 84779.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.042645 restraints weight = 73269.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.042980 restraints weight = 64700.224| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17078 Z= 0.175 Angle : 0.687 16.043 23117 Z= 0.336 Chirality : 0.042 0.264 2641 Planarity : 0.004 0.053 2912 Dihedral : 7.438 78.170 2296 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.72 % Allowed : 16.95 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 2005 helix: 0.64 (0.15), residues: 1191 sheet: 0.34 (0.39), residues: 177 loop : -1.19 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 205 TYR 0.015 0.002 TYR D 399 PHE 0.019 0.002 PHE E 328 TRP 0.024 0.002 TRP B 445 HIS 0.010 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00383 (17078) covalent geometry : angle 0.68712 (23117) hydrogen bonds : bond 0.03762 ( 804) hydrogen bonds : angle 4.30818 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8273 (mmt180) cc_final: 0.8021 (mmt180) REVERT: A 816 MET cc_start: 0.8161 (ptp) cc_final: 0.7871 (ptp) REVERT: A 852 ASP cc_start: 0.9200 (m-30) cc_final: 0.8713 (p0) REVERT: B 287 LEU cc_start: 0.9539 (mm) cc_final: 0.9230 (pp) REVERT: B 409 ILE cc_start: 0.9149 (mm) cc_final: 0.8856 (pt) REVERT: B 432 MET cc_start: 0.8158 (ptp) cc_final: 0.7555 (ptp) REVERT: B 433 TRP cc_start: 0.8623 (p90) cc_final: 0.8265 (p90) REVERT: C 24 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.4213 (mm) REVERT: C 29 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: C 189 MET cc_start: 0.8268 (mmt) cc_final: 0.8016 (mmt) REVERT: C 365 ASN cc_start: 0.8922 (t0) cc_final: 0.8550 (m-40) REVERT: C 394 LEU cc_start: 0.9018 (tp) cc_final: 0.8723 (mt) REVERT: C 462 MET cc_start: 0.6581 (pmm) cc_final: 0.6273 (pmm) REVERT: C 634 TYR cc_start: 0.8574 (t80) cc_final: 0.8279 (t80) REVERT: D 51 LEU cc_start: 0.9829 (mt) cc_final: 0.9401 (pp) REVERT: D 64 LEU cc_start: 0.9538 (mt) cc_final: 0.9336 (tt) REVERT: D 168 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8162 (pttp) REVERT: D 373 MET cc_start: 0.8832 (tmm) cc_final: 0.8420 (ptt) REVERT: D 388 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6564 (mpp) REVERT: E 133 MET cc_start: 0.8409 (ttm) cc_final: 0.7849 (mmm) outliers start: 51 outliers final: 34 residues processed: 171 average time/residue: 0.1109 time to fit residues: 30.4928 Evaluate side-chains 161 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 336 PHE Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 92 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS C 240 HIS ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 HIS ** 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 = 0.3735 r_free = 0.3735 target = 0.058605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.042865 restraints weight = 141495.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.043655 restraints weight = 101138.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.044225 restraints weight = 80018.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.044551 restraints weight = 68253.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.044802 restraints weight = 61317.997| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17078 Z= 0.109 Angle : 0.660 13.139 23117 Z= 0.312 Chirality : 0.041 0.213 2641 Planarity : 0.004 0.052 2912 Dihedral : 7.103 78.164 2296 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.76 % Allowed : 17.80 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2005 helix: 0.94 (0.15), residues: 1193 sheet: 0.78 (0.40), residues: 166 loop : -1.06 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 546 TYR 0.014 0.001 TYR E 269 PHE 0.024 0.001 PHE C 479 TRP 0.016 0.001 TRP B 445 HIS 0.016 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00238 (17078) covalent geometry : angle 0.66014 (23117) hydrogen bonds : bond 0.03331 ( 804) hydrogen bonds : angle 4.07740 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8134 (mmt180) cc_final: 0.7840 (mmt180) REVERT: A 752 MET cc_start: 0.6066 (ppp) cc_final: 0.5859 (ppp) REVERT: A 816 MET cc_start: 0.8309 (ptp) cc_final: 0.7528 (ptp) REVERT: A 820 MET cc_start: 0.9343 (ptp) cc_final: 0.8709 (mpp) REVERT: A 852 ASP cc_start: 0.9151 (m-30) cc_final: 0.8718 (p0) REVERT: B 287 LEU cc_start: 0.9547 (mm) cc_final: 0.9215 (pp) REVERT: B 409 ILE cc_start: 0.9135 (mm) cc_final: 0.8877 (pt) REVERT: B 432 MET cc_start: 0.8221 (ptp) cc_final: 0.7693 (ptp) REVERT: B 433 TRP cc_start: 0.8504 (p90) cc_final: 0.8031 (p90) REVERT: C 24 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.4119 (mm) REVERT: C 29 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: C 178 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7673 (t70) REVERT: C 189 MET cc_start: 0.8269 (mmt) cc_final: 0.7978 (mmt) REVERT: C 365 ASN cc_start: 0.8792 (t0) cc_final: 0.8484 (m-40) REVERT: C 394 LEU cc_start: 0.8987 (tp) cc_final: 0.8686 (mt) REVERT: C 462 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.6139 (pmm) REVERT: C 469 MET cc_start: 0.8858 (tmm) cc_final: 0.8064 (ppp) REVERT: C 592 LEU cc_start: 0.8990 (mm) cc_final: 0.8748 (mm) REVERT: C 634 TYR cc_start: 0.8473 (t80) cc_final: 0.8137 (t80) REVERT: D 75 MET cc_start: 0.8866 (ttp) cc_final: 0.8438 (ptm) REVERT: D 168 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (pttp) REVERT: D 373 MET cc_start: 0.8828 (tmm) cc_final: 0.8495 (ptt) REVERT: D 388 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5994 (mpp) REVERT: E 133 MET cc_start: 0.8568 (ttm) cc_final: 0.7781 (mmm) outliers start: 33 outliers final: 24 residues processed: 164 average time/residue: 0.1176 time to fit residues: 31.0857 Evaluate side-chains 157 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 157 optimal weight: 8.9990 chunk 116 optimal weight: 0.0270 chunk 68 optimal weight: 4.9990 chunk 181 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.043230 restraints weight = 153932.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.043992 restraints weight = 107161.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.044609 restraints weight = 84453.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.044983 restraints weight = 70811.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045157 restraints weight = 63050.348| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17078 Z= 0.118 Angle : 0.648 13.342 23117 Z= 0.309 Chirality : 0.040 0.202 2641 Planarity : 0.004 0.051 2912 Dihedral : 7.046 75.027 2296 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.92 % Allowed : 18.18 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 2005 helix: 1.06 (0.15), residues: 1187 sheet: 0.75 (0.40), residues: 166 loop : -1.00 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 546 TYR 0.018 0.001 TYR D 399 PHE 0.023 0.001 PHE C 479 TRP 0.017 0.001 TRP B 445 HIS 0.013 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00259 (17078) covalent geometry : angle 0.64753 (23117) hydrogen bonds : bond 0.03271 ( 804) hydrogen bonds : angle 4.05120 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 ARG cc_start: 0.8197 (mmt180) cc_final: 0.7886 (mmt180) REVERT: A 816 MET cc_start: 0.8241 (ptp) cc_final: 0.7497 (ptp) REVERT: A 820 MET cc_start: 0.9330 (ptp) cc_final: 0.8726 (mpp) REVERT: A 852 ASP cc_start: 0.9207 (m-30) cc_final: 0.8766 (p0) REVERT: B 287 LEU cc_start: 0.9538 (mm) cc_final: 0.9175 (pp) REVERT: B 409 ILE cc_start: 0.9168 (mm) cc_final: 0.8910 (pt) REVERT: B 432 MET cc_start: 0.8154 (ptp) cc_final: 0.7662 (ptp) REVERT: B 433 TRP cc_start: 0.8592 (p90) cc_final: 0.8173 (p90) REVERT: C 24 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5333 (mm) REVERT: C 178 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.7860 (t70) REVERT: C 189 MET cc_start: 0.8213 (mmt) cc_final: 0.7918 (mmt) REVERT: C 365 ASN cc_start: 0.8850 (t0) cc_final: 0.8524 (m-40) REVERT: C 394 LEU cc_start: 0.8998 (tp) cc_final: 0.8710 (mt) REVERT: C 592 LEU cc_start: 0.8978 (mm) cc_final: 0.8760 (mm) REVERT: C 610 TYR cc_start: 0.8703 (m-80) cc_final: 0.8373 (m-10) REVERT: C 634 TYR cc_start: 0.8579 (t80) cc_final: 0.8247 (t80) REVERT: D 75 MET cc_start: 0.8899 (ttp) cc_final: 0.8678 (ptm) REVERT: D 303 MET cc_start: 0.9200 (ptp) cc_final: 0.8920 (ppp) REVERT: D 373 MET cc_start: 0.8806 (tmm) cc_final: 0.8507 (ptt) REVERT: D 388 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6210 (mpp) REVERT: E 133 MET cc_start: 0.8652 (ttm) cc_final: 0.7892 (mmm) outliers start: 36 outliers final: 27 residues processed: 160 average time/residue: 0.1105 time to fit residues: 28.6865 Evaluate side-chains 160 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 53 optimal weight: 7.9990 chunk 197 optimal weight: 0.0060 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 92 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 overall best weight: 2.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.057090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.041540 restraints weight = 143329.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.042388 restraints weight = 102963.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.042890 restraints weight = 82132.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.043246 restraints weight = 70877.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.043484 restraints weight = 63792.670| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17078 Z= 0.142 Angle : 0.679 13.237 23117 Z= 0.325 Chirality : 0.041 0.231 2641 Planarity : 0.004 0.051 2912 Dihedral : 7.156 74.027 2296 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.76 % Allowed : 18.39 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 2005 helix: 0.93 (0.15), residues: 1193 sheet: 0.50 (0.39), residues: 175 loop : -1.01 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 205 TYR 0.023 0.001 TYR D 399 PHE 0.023 0.001 PHE C 479 TRP 0.019 0.001 TRP B 445 HIS 0.011 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00311 (17078) covalent geometry : angle 0.67883 (23117) hydrogen bonds : bond 0.03430 ( 804) hydrogen bonds : angle 4.12655 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 852 ASP cc_start: 0.9092 (m-30) cc_final: 0.8668 (p0) REVERT: B 287 LEU cc_start: 0.9554 (mm) cc_final: 0.9206 (pp) REVERT: B 409 ILE cc_start: 0.9178 (mm) cc_final: 0.8914 (pt) REVERT: B 432 MET cc_start: 0.8150 (ptp) cc_final: 0.7512 (ptp) REVERT: B 433 TRP cc_start: 0.8589 (p90) cc_final: 0.8228 (p90) REVERT: C 189 MET cc_start: 0.8267 (mmt) cc_final: 0.7943 (mmt) REVERT: C 365 ASN cc_start: 0.8934 (t0) cc_final: 0.8569 (m-40) REVERT: C 394 LEU cc_start: 0.9043 (tp) cc_final: 0.8764 (mt) REVERT: C 467 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8671 (pp20) REVERT: C 592 LEU cc_start: 0.9040 (mm) cc_final: 0.8794 (mm) REVERT: C 610 TYR cc_start: 0.8670 (m-80) cc_final: 0.8356 (m-10) REVERT: C 634 TYR cc_start: 0.8719 (t80) cc_final: 0.8401 (t80) REVERT: D 85 MET cc_start: 0.8847 (mmm) cc_final: 0.8278 (mmm) REVERT: D 168 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8118 (pttp) REVERT: D 303 MET cc_start: 0.9187 (ptp) cc_final: 0.8923 (ppp) REVERT: D 373 MET cc_start: 0.8834 (tmm) cc_final: 0.8548 (ptt) REVERT: D 388 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6385 (mpp) REVERT: E 133 MET cc_start: 0.8564 (ttm) cc_final: 0.7777 (mmm) REVERT: E 263 LYS cc_start: 0.9061 (pttm) cc_final: 0.8791 (mptt) outliers start: 33 outliers final: 28 residues processed: 158 average time/residue: 0.1128 time to fit residues: 28.6351 Evaluate side-chains 156 residues out of total 1878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 440 CYS Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 371 ASP Chi-restraints excluded: chain E residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 50 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.055958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.040809 restraints weight = 140791.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.041536 restraints weight = 102197.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.041913 restraints weight = 81026.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.042305 restraints weight = 70084.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.042581 restraints weight = 63331.095| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17078 Z= 0.171 Angle : 0.718 13.758 23117 Z= 0.346 Chirality : 0.042 0.224 2641 Planarity : 0.004 0.052 2912 Dihedral : 7.334 75.033 2296 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.81 % Allowed : 18.44 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 2005 helix: 0.75 (0.15), residues: 1192 sheet: 0.41 (0.39), residues: 175 loop : -1.05 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 205 TYR 0.026 0.002 TYR D 399 PHE 0.022 0.002 PHE C 479 TRP 0.022 0.002 TRP B 445 HIS 0.011 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00371 (17078) covalent geometry : angle 0.71769 (23117) hydrogen bonds : bond 0.03637 ( 804) hydrogen bonds : angle 4.28210 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.05 seconds wall clock time: 51 minutes 16.26 seconds (3076.26 seconds total)