Starting phenix.real_space_refine on Fri Jul 3 01:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4g_70100/07_2026/9o4g_70100.map" } resolution = 3.42 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= 0.045 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 Mn 2 7.51 5 P 2 5.49 5 S 51 5.16 5 C 6982 2.51 5 N 1960 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10989 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5742 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 667} Chain: "B" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5220 Classifications: {'peptide': 664} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 615} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 2.36, per 1000 atoms: 0.21 Number of scatterers: 10989 At special positions: 0 Unit cell: (99.544, 109.282, 127.676, 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) Mn 2 24.99 S 51 16.00 P 2 15.00 O 1992 8.00 N 1960 7.00 C 6982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 784 " distance=2.03 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 850 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 405 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 678 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 314.0 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 14 sheets defined 40.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.818A pdb=" N LEU A 251 " --> pdb=" O HIS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.814A pdb=" N LEU A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.602A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.842A pdb=" N GLU A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.583A pdb=" N ARG A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 376 " --> pdb=" O HIS A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 376' Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.724A pdb=" N ALA A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 401 through 435 removed outlier: 3.542A pdb=" N ASN A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.645A pdb=" N GLN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.667A pdb=" N LEU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 597 removed outlier: 3.966A pdb=" N SER A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 596 " --> pdb=" O GLN A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 605 removed outlier: 3.888A pdb=" N ILE A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 removed outlier: 4.370A pdb=" N GLY A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.728A pdb=" N ARG A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.811A pdb=" N GLY A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 708 No H-bonds generated for 'chain 'A' and resid 706 through 708' Processing helix chain 'A' and resid 725 through 734 removed outlier: 4.243A pdb=" N GLN A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 787 through 794 Processing helix chain 'A' and resid 804 through 817 Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 846 through 858 removed outlier: 3.995A pdb=" N GLY A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 853 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 873 Processing helix chain 'B' and resid 108 through 114 removed outlier: 3.954A pdb=" N GLU B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.582A pdb=" N ALA B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 188 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.589A pdb=" N GLN B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.503A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.551A pdb=" N TRP B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.510A pdb=" N SER B 320 " --> pdb=" O HIS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.846A pdb=" N HIS B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.540A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 353 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 361 " --> pdb=" O TRP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.173A pdb=" N GLN B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 removed outlier: 4.048A pdb=" N VAL B 391 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 438 removed outlier: 4.282A pdb=" N ALA B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 520 No H-bonds generated for 'chain 'B' and resid 518 through 520' Processing helix chain 'B' and resid 521 through 534 removed outlier: 3.618A pdb=" N PHE B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 563 through 577 Processing helix chain 'B' and resid 593 through 603 Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.673A pdb=" N LEU B 625 " --> pdb=" O THR B 621 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 627 " --> pdb=" O ASP B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 695 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.942A pdb=" N GLU B 703 " --> pdb=" O GLU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.535A pdb=" N GLY B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 3.604A pdb=" N LEU B 765 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 225 removed outlier: 6.620A pdb=" N TYR A 174 " --> pdb=" O MET A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.651A pdb=" N HIS A 394 " --> pdb=" O HIS A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 484 through 486 removed outlier: 3.618A pdb=" N PHE A 468 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 518 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS A 546 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LYS A 520 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU A 544 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE A 522 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 542 " --> pdb=" O ILE A 522 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 524 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 537 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 555 " --> pdb=" O TYR A 545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 574 removed outlier: 3.730A pdb=" N LEU B 487 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 463 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET B 461 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 460 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG B 454 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 462 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 452 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 464 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 450 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 466 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 448 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN B 468 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE B 455 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG B 393 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 394 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 823 " --> pdb=" O TRP B 394 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 396 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN A 825 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 574 removed outlier: 3.730A pdb=" N LEU B 487 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 463 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET B 461 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 460 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG B 454 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B 462 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 452 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 464 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 450 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 466 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 448 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN B 468 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE B 455 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ARG B 393 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP B 394 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 823 " --> pdb=" O TRP B 394 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR B 396 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN A 825 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 10.817A pdb=" N VAL A 741 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N GLN A 825 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N TYR A 743 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N VAL A 827 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N ILE A 745 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 829 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 747 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 746 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 686 through 689 removed outlier: 9.025A pdb=" N THR A 687 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 654 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 689 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 656 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 783 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 167 removed outlier: 8.520A pdb=" N VAL B 149 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 121 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 151 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 123 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG B 118 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 196 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 230 Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AB3, first strand: chain 'B' and resid 587 through 588 removed outlier: 3.591A pdb=" N LEU B 548 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR B 509 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ALA B 614 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 511 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 637 through 639 removed outlier: 6.617A pdb=" N ALA B 638 " --> pdb=" O LEU B 720 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 669 removed outlier: 6.375A pdb=" N PHE B 644 " --> pdb=" O GLN B 729 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3685 1.34 - 1.46: 2588 1.46 - 1.59: 4911 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 11266 Sorted by residual: bond pdb=" N VAL A 836 " pdb=" CA VAL A 836 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.15e-02 7.56e+03 1.11e+00 bond pdb=" CA VAL A 326 " pdb=" C VAL A 326 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.11e+00 bond pdb=" C PHE B 679 " pdb=" N TYR B 680 " ideal model delta sigma weight residual 1.325 1.335 -0.010 1.14e-02 7.69e+03 8.10e-01 bond pdb=" CB GLN B 187 " pdb=" CG GLN B 187 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" CA ASN A 396 " pdb=" C ASN A 396 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.40e-02 5.10e+03 6.97e-01 ... (remaining 11261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 15027 1.97 - 3.95: 225 3.95 - 5.92: 18 5.92 - 7.90: 2 7.90 - 9.87: 1 Bond angle restraints: 15273 Sorted by residual: angle pdb=" C MET A 325 " pdb=" N VAL A 326 " pdb=" CA VAL A 326 " ideal model delta sigma weight residual 120.24 123.47 -3.23 6.30e-01 2.52e+00 2.62e+01 angle pdb=" C TYR B 680 " pdb=" CA TYR B 680 " pdb=" CB TYR B 680 " ideal model delta sigma weight residual 115.79 111.01 4.78 1.19e+00 7.06e-01 1.61e+01 angle pdb=" C VAL A 326 " pdb=" CA VAL A 326 " pdb=" CB VAL A 326 " ideal model delta sigma weight residual 114.35 111.21 3.14 1.06e+00 8.90e-01 8.78e+00 angle pdb=" CA LEU A 699 " pdb=" CB LEU A 699 " pdb=" CG LEU A 699 " ideal model delta sigma weight residual 116.30 126.17 -9.87 3.50e+00 8.16e-02 7.96e+00 angle pdb=" N GLY A 298 " pdb=" CA GLY A 298 " pdb=" C GLY A 298 " ideal model delta sigma weight residual 114.67 111.12 3.55 1.41e+00 5.03e-01 6.35e+00 ... (remaining 15268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6034 17.96 - 35.91: 589 35.91 - 53.87: 149 53.87 - 71.83: 22 71.83 - 89.79: 18 Dihedral angle restraints: 6812 sinusoidal: 2850 harmonic: 3962 Sorted by residual: dihedral pdb=" CB CYS A 838 " pdb=" SG CYS A 838 " pdb=" SG CYS A 850 " pdb=" CB CYS A 850 " ideal model delta sinusoidal sigma weight residual 93.00 164.61 -71.61 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS B 628 " pdb=" SG CYS B 628 " pdb=" SG CYS B 678 " pdb=" CB CYS B 678 " ideal model delta sinusoidal sigma weight residual -86.00 -124.42 38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 784 " pdb=" CB CYS A 784 " ideal model delta sinusoidal sigma weight residual -86.00 -121.68 35.68 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 6809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 993 0.032 - 0.063: 451 0.063 - 0.095: 126 0.095 - 0.127: 65 0.127 - 0.159: 1 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CA ILE B 379 " pdb=" N ILE B 379 " pdb=" C ILE B 379 " pdb=" CB ILE B 379 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA PRO A 844 " pdb=" N PRO A 844 " pdb=" C PRO A 844 " pdb=" CB PRO A 844 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE A 449 " pdb=" N ILE A 449 " pdb=" C ILE A 449 " pdb=" CB ILE A 449 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1633 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 449 " 0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 450 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 130 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 131 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 843 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO A 844 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 844 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 844 " 0.026 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1398 2.75 - 3.29: 9732 3.29 - 3.83: 16227 3.83 - 4.36: 18775 4.36 - 4.90: 33307 Nonbonded interactions: 79439 Sorted by model distance: nonbonded pdb=" OD2 ASP A 261 " pdb="MN MN A 901 " model vdw 2.218 3.060 nonbonded pdb=" OD2 ASP A 263 " pdb="MN MN A 901 " model vdw 2.232 3.060 nonbonded pdb=" NE2 HIS A 394 " pdb="MN MN A 901 " model vdw 2.276 3.140 nonbonded pdb=" NE2 HIS A 831 " pdb="MN MN A 902 " model vdw 2.331 3.140 nonbonded pdb="MN MN A 901 " pdb=" O2A UDP A 903 " model vdw 2.356 3.060 ... (remaining 79434 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 individual isotropic 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: 1.050 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.003 0.028 11272 Z= 0.159 Angle : 0.607 9.872 15285 Z= 0.344 Chirality : 0.041 0.159 1636 Planarity : 0.005 0.056 2004 Dihedral : 15.602 89.787 4250 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.71 % Allowed : 11.85 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.85 (0.23), residues: 1364 helix: 0.09 (0.26), residues: 438 sheet: -0.76 (0.35), residues: 221 loop : -0.85 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 507 TYR 0.020 0.001 TYR A 743 PHE 0.023 0.001 PHE A 695 TRP 0.014 0.002 TRP B 357 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (11266) covalent geometry : angle 0.60731 / 0.34 (15273) SS BOND : bond 0.00156 / 0.08 ( 6) SS BOND : angle 0.70383 / 0.39 ( 12) hydrogen bonds : bond 0.20154 / 12.58 ( 394) hydrogen bonds : angle 7.86579 / 5.39 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: A 544 LEU cc_start: 0.7162 (mt) cc_final: 0.6901 (mp) REVERT: A 675 LYS cc_start: 0.7636 (mttt) cc_final: 0.6977 (mmtt) REVERT: A 685 GLU cc_start: 0.6267 (mp0) cc_final: 0.5888 (mp0) REVERT: A 751 ASP cc_start: 0.7381 (t70) cc_final: 0.6374 (p0) REVERT: A 777 ASP cc_start: 0.8043 (t70) cc_final: 0.7413 (p0) REVERT: B 262 HIS cc_start: 0.6726 (m-70) cc_final: 0.6427 (m-70) REVERT: B 419 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7288 (tpt-90) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.1074 time to fit residues: 18.6946 Evaluate side-chains 124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 643 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN B 718 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.201655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159089 restraints weight = 12714.201| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.94 r_work: 0.3879 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11272 Z= 0.144 Angle : 0.538 7.868 15285 Z= 0.279 Chirality : 0.042 0.142 1636 Planarity : 0.005 0.055 2004 Dihedral : 6.991 56.561 1591 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.73 % Allowed : 11.34 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.97 (0.22), residues: 1364 helix: -0.06 (0.25), residues: 467 sheet: -0.57 (0.36), residues: 209 loop : -1.01 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 483 TYR 0.020 0.002 TYR A 743 PHE 0.018 0.001 PHE A 468 TRP 0.012 0.002 TRP A 359 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (11266) covalent geometry : angle 0.53739 / 0.28 (15273) SS BOND : bond 0.00155 / 0.07 ( 6) SS BOND : angle 0.72317 / 0.39 ( 12) hydrogen bonds : bond 0.04704 / 3.06 ( 394) hydrogen bonds : angle 5.65301 / 3.87 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6407 (ttm-80) cc_final: 0.6169 (ttm-80) REVERT: A 310 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7511 (ttm) REVERT: A 325 MET cc_start: 0.5213 (ttp) cc_final: 0.4923 (ttt) REVERT: A 331 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: A 438 GLU cc_start: 0.7009 (pm20) cc_final: 0.6573 (pm20) REVERT: A 675 LYS cc_start: 0.7538 (mttt) cc_final: 0.6952 (mmtt) REVERT: A 685 GLU cc_start: 0.6205 (mp0) cc_final: 0.5649 (mp0) REVERT: A 751 ASP cc_start: 0.7238 (t70) cc_final: 0.6286 (p0) REVERT: A 777 ASP cc_start: 0.8133 (t70) cc_final: 0.7581 (p0) REVERT: A 847 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.3588 (m-10) REVERT: B 191 ASP cc_start: 0.9165 (t0) cc_final: 0.8789 (t0) REVERT: B 262 HIS cc_start: 0.7035 (m-70) cc_final: 0.6750 (m-70) REVERT: B 349 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.5876 (t80) REVERT: B 419 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (tpt90) REVERT: B 645 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7268 (tm-30) outliers start: 32 outliers final: 20 residues processed: 140 average time/residue: 0.1025 time to fit residues: 20.0591 Evaluate side-chains 136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS B 718 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.203389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.161511 restraints weight = 12724.815| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.01 r_work: 0.3907 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11272 Z= 0.108 Angle : 0.480 5.873 15285 Z= 0.249 Chirality : 0.041 0.146 1636 Planarity : 0.004 0.055 2004 Dihedral : 6.407 58.249 1575 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.07 % Allowed : 11.85 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.86 (0.23), residues: 1364 helix: 0.12 (0.25), residues: 468 sheet: -0.64 (0.36), residues: 201 loop : -0.97 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.020 0.001 TYR A 743 PHE 0.012 0.001 PHE A 468 TRP 0.009 0.001 TRP A 359 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11266) covalent geometry : angle 0.48019 / 0.25 (15273) SS BOND : bond 0.00109 / 0.05 ( 6) SS BOND : angle 0.64392 / 0.36 ( 12) hydrogen bonds : bond 0.03936 / 2.55 ( 394) hydrogen bonds : angle 5.13073 / 3.52 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6367 (ttm-80) cc_final: 0.5975 (ttt90) REVERT: A 310 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7435 (ttm) REVERT: A 325 MET cc_start: 0.5060 (ttp) cc_final: 0.4809 (ttt) REVERT: A 331 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: A 336 MET cc_start: 0.6853 (mtm) cc_final: 0.6437 (mtp) REVERT: A 675 LYS cc_start: 0.7632 (mttt) cc_final: 0.7050 (mmtt) REVERT: A 685 GLU cc_start: 0.6149 (mp0) cc_final: 0.5677 (mp0) REVERT: A 751 ASP cc_start: 0.7084 (t70) cc_final: 0.6159 (p0) REVERT: A 777 ASP cc_start: 0.8147 (t70) cc_final: 0.7558 (p0) REVERT: A 847 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.3692 (m-10) REVERT: B 191 ASP cc_start: 0.9157 (t0) cc_final: 0.8753 (t0) REVERT: B 262 HIS cc_start: 0.7022 (m-70) cc_final: 0.6746 (m-70) REVERT: B 645 GLN cc_start: 0.7509 (tm-30) cc_final: 0.7209 (tm-30) outliers start: 36 outliers final: 21 residues processed: 138 average time/residue: 0.1066 time to fit residues: 20.8239 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 569 HIS B 718 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.206425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164850 restraints weight = 12813.112| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.95 r_work: 0.3915 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11272 Z= 0.128 Angle : 0.496 6.055 15285 Z= 0.256 Chirality : 0.041 0.152 1636 Planarity : 0.004 0.054 2004 Dihedral : 6.266 54.707 1569 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.07 % Allowed : 12.62 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.87 (0.23), residues: 1364 helix: 0.21 (0.25), residues: 465 sheet: -0.73 (0.36), residues: 206 loop : -1.03 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 483 TYR 0.023 0.001 TYR A 743 PHE 0.015 0.001 PHE A 468 TRP 0.012 0.001 TRP A 359 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11266) covalent geometry : angle 0.49572 / 0.26 (15273) SS BOND : bond 0.00132 / 0.07 ( 6) SS BOND : angle 0.77633 / 0.42 ( 12) hydrogen bonds : bond 0.03906 / 2.54 ( 394) hydrogen bonds : angle 5.02488 / 3.43 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6589 (ttm-80) cc_final: 0.6149 (ttt90) REVERT: A 258 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5798 (ttm) REVERT: A 310 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7399 (ttm) REVERT: A 325 MET cc_start: 0.5080 (ttp) cc_final: 0.4807 (ttt) REVERT: A 331 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: A 336 MET cc_start: 0.6925 (mtm) cc_final: 0.6506 (mtp) REVERT: A 469 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (pp) REVERT: A 675 LYS cc_start: 0.7656 (mttt) cc_final: 0.7047 (mmtt) REVERT: A 685 GLU cc_start: 0.6204 (mp0) cc_final: 0.5691 (mp0) REVERT: A 751 ASP cc_start: 0.7098 (t70) cc_final: 0.6185 (p0) REVERT: A 777 ASP cc_start: 0.8176 (t70) cc_final: 0.7581 (p0) REVERT: A 847 TYR cc_start: 0.4912 (OUTLIER) cc_final: 0.3800 (m-10) REVERT: B 191 ASP cc_start: 0.9108 (t0) cc_final: 0.8725 (t0) REVERT: B 262 HIS cc_start: 0.7022 (m-70) cc_final: 0.6751 (m-70) REVERT: B 461 MET cc_start: 0.8050 (mmm) cc_final: 0.7804 (ttm) REVERT: B 600 LEU cc_start: 0.7068 (mt) cc_final: 0.6820 (tp) outliers start: 36 outliers final: 26 residues processed: 130 average time/residue: 0.1003 time to fit residues: 18.8092 Evaluate side-chains 130 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 HIS A 370 ASN A 507 ASN B 569 HIS B 718 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.200702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159283 restraints weight = 12864.863| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.88 r_work: 0.3776 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11272 Z= 0.246 Angle : 0.641 6.923 15285 Z= 0.332 Chirality : 0.046 0.167 1636 Planarity : 0.005 0.052 2004 Dihedral : 6.906 51.499 1569 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.52 % Allowed : 12.62 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.40 (0.22), residues: 1364 helix: -0.21 (0.25), residues: 456 sheet: -1.06 (0.36), residues: 203 loop : -1.34 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 388 TYR 0.030 0.002 TYR A 743 PHE 0.026 0.002 PHE A 468 TRP 0.021 0.002 TRP A 359 HIS 0.007 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 (11266) covalent geometry : angle 0.64110 / 0.33 (15273) SS BOND : bond 0.00326 / 0.17 ( 6) SS BOND : angle 0.83345 / 0.48 ( 12) hydrogen bonds : bond 0.05094 / 3.32 ( 394) hydrogen bonds : angle 5.44403 / 3.72 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6488 (ttm-80) cc_final: 0.5997 (ttt90) REVERT: A 331 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 469 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (pp) REVERT: A 675 LYS cc_start: 0.7567 (mttt) cc_final: 0.6935 (mmtt) REVERT: A 685 GLU cc_start: 0.6310 (mp0) cc_final: 0.5688 (mp0) REVERT: A 751 ASP cc_start: 0.7224 (t70) cc_final: 0.6987 (t70) REVERT: A 777 ASP cc_start: 0.8210 (t70) cc_final: 0.7683 (p0) REVERT: A 847 TYR cc_start: 0.4871 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: B 191 ASP cc_start: 0.9164 (t0) cc_final: 0.8781 (t0) REVERT: B 262 HIS cc_start: 0.7101 (m-70) cc_final: 0.6848 (m-70) REVERT: B 630 MET cc_start: 0.8434 (mmm) cc_final: 0.8046 (mmm) REVERT: B 645 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7351 (tm-30) REVERT: B 756 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (tt) outliers start: 53 outliers final: 35 residues processed: 153 average time/residue: 0.0918 time to fit residues: 20.1792 Evaluate side-chains 139 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 0.0050 chunk 123 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 72 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN A 507 ASN B 569 HIS ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.207315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165609 restraints weight = 12761.039| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.91 r_work: 0.3851 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11272 Z= 0.094 Angle : 0.485 6.701 15285 Z= 0.248 Chirality : 0.040 0.151 1636 Planarity : 0.004 0.053 2004 Dihedral : 6.208 47.501 1569 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.64 % Allowed : 15.17 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.01 (0.22), residues: 1364 helix: 0.23 (0.26), residues: 459 sheet: -0.83 (0.34), residues: 213 loop : -1.21 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 388 TYR 0.016 0.001 TYR A 743 PHE 0.009 0.001 PHE A 468 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.000 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (11266) covalent geometry : angle 0.48446 / 0.25 (15273) SS BOND : bond 0.00086 / 0.04 ( 6) SS BOND : angle 0.61453 / 0.35 ( 12) hydrogen bonds : bond 0.03473 / 2.26 ( 394) hydrogen bonds : angle 4.85160 / 3.34 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6517 (ttm-80) cc_final: 0.6117 (ttt90) REVERT: A 331 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: A 465 GLU cc_start: 0.8251 (mp0) cc_final: 0.7983 (mt-10) REVERT: A 469 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8099 (pp) REVERT: A 675 LYS cc_start: 0.7663 (mttt) cc_final: 0.6950 (tptt) REVERT: A 677 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.6427 (t80) REVERT: A 685 GLU cc_start: 0.6273 (mp0) cc_final: 0.5747 (mp0) REVERT: A 743 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7104 (m-10) REVERT: A 751 ASP cc_start: 0.7011 (t70) cc_final: 0.6100 (p0) REVERT: A 777 ASP cc_start: 0.8218 (t70) cc_final: 0.7653 (p0) REVERT: A 847 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.3798 (m-10) REVERT: B 191 ASP cc_start: 0.9158 (t0) cc_final: 0.8736 (t0) REVERT: B 600 LEU cc_start: 0.7391 (mt) cc_final: 0.6975 (tp) REVERT: B 645 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7199 (tm-30) outliers start: 31 outliers final: 23 residues processed: 136 average time/residue: 0.0850 time to fit residues: 16.9288 Evaluate side-chains 133 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 0.0980 chunk 106 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 507 ASN B 569 HIS ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.208216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166808 restraints weight = 12604.289| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.81 r_work: 0.3931 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11272 Z= 0.092 Angle : 0.477 9.374 15285 Z= 0.241 Chirality : 0.040 0.155 1636 Planarity : 0.004 0.054 2004 Dihedral : 6.030 47.253 1569 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.39 % Allowed : 15.60 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.86 (0.23), residues: 1364 helix: 0.42 (0.26), residues: 463 sheet: -0.84 (0.35), residues: 206 loop : -1.13 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 388 TYR 0.015 0.001 TYR A 743 PHE 0.011 0.001 PHE A 641 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.000 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (11266) covalent geometry : angle 0.47716 / 0.24 (15273) SS BOND : bond 0.00163 / 0.08 ( 6) SS BOND : angle 0.61878 / 0.35 ( 12) hydrogen bonds : bond 0.03296 / 2.15 ( 394) hydrogen bonds : angle 4.70793 / 3.24 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6548 (ttm-80) cc_final: 0.6210 (ttt90) REVERT: A 331 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: A 677 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.6409 (t80) REVERT: A 685 GLU cc_start: 0.6152 (mp0) cc_final: 0.5686 (mp0) REVERT: A 743 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7163 (m-10) REVERT: A 751 ASP cc_start: 0.6945 (t70) cc_final: 0.6059 (p0) REVERT: A 777 ASP cc_start: 0.8175 (t70) cc_final: 0.7660 (p0) REVERT: A 847 TYR cc_start: 0.4976 (OUTLIER) cc_final: 0.3786 (m-10) REVERT: B 191 ASP cc_start: 0.9173 (t0) cc_final: 0.8727 (t0) REVERT: B 388 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7828 (ttp-110) REVERT: B 395 ASP cc_start: 0.7728 (m-30) cc_final: 0.7527 (m-30) REVERT: B 600 LEU cc_start: 0.7324 (mt) cc_final: 0.6966 (tp) outliers start: 28 outliers final: 21 residues processed: 125 average time/residue: 0.0930 time to fit residues: 16.7459 Evaluate side-chains 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN B 569 HIS B 718 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.191176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149444 restraints weight = 12511.898| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.07 r_work: 0.3705 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11272 Z= 0.131 Angle : 0.517 8.592 15285 Z= 0.260 Chirality : 0.041 0.166 1636 Planarity : 0.005 0.053 2004 Dihedral : 6.131 48.342 1567 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.15 % Allowed : 14.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.93 (0.23), residues: 1364 helix: 0.36 (0.26), residues: 461 sheet: -0.85 (0.35), residues: 207 loop : -1.19 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 507 TYR 0.017 0.001 TYR A 811 PHE 0.015 0.001 PHE A 468 TRP 0.011 0.001 TRP A 359 HIS 0.004 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (11266) covalent geometry : angle 0.51735 / 0.26 (15273) SS BOND : bond 0.00181 / 0.09 ( 6) SS BOND : angle 0.58914 / 0.33 ( 12) hydrogen bonds : bond 0.03702 / 2.41 ( 394) hydrogen bonds : angle 4.81004 / 3.30 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6528 (ttm-80) cc_final: 0.6176 (ttt90) REVERT: A 325 MET cc_start: 0.5107 (ttp) cc_final: 0.4673 (ttt) REVERT: A 331 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: A 677 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6689 (t80) REVERT: A 685 GLU cc_start: 0.6279 (mp0) cc_final: 0.5691 (mp0) REVERT: A 743 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7359 (m-10) REVERT: A 751 ASP cc_start: 0.6977 (t70) cc_final: 0.6673 (t70) REVERT: A 777 ASP cc_start: 0.8138 (t70) cc_final: 0.7585 (p0) REVERT: A 847 TYR cc_start: 0.4842 (OUTLIER) cc_final: 0.3693 (m-10) REVERT: B 191 ASP cc_start: 0.9200 (t0) cc_final: 0.8735 (t0) REVERT: B 388 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7755 (ttp-110) REVERT: B 576 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5992 (mtm110) REVERT: B 600 LEU cc_start: 0.7313 (mt) cc_final: 0.6934 (tp) outliers start: 37 outliers final: 28 residues processed: 128 average time/residue: 0.0874 time to fit residues: 16.0726 Evaluate side-chains 132 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 576 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 643 HIS Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.0020 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN A 507 ASN B 569 HIS ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.193029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151437 restraints weight = 12320.193| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.97 r_work: 0.3730 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11272 Z= 0.098 Angle : 0.483 8.638 15285 Z= 0.243 Chirality : 0.040 0.154 1636 Planarity : 0.004 0.053 2004 Dihedral : 5.954 48.146 1567 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.15 % Allowed : 14.75 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.77 (0.23), residues: 1364 helix: 0.53 (0.26), residues: 458 sheet: -0.79 (0.35), residues: 207 loop : -1.11 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 507 TYR 0.014 0.001 TYR A 811 PHE 0.014 0.001 PHE A 352 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11266) covalent geometry : angle 0.48317 / 0.24 (15273) SS BOND : bond 0.00167 / 0.08 ( 6) SS BOND : angle 0.61781 / 0.35 ( 12) hydrogen bonds : bond 0.03313 / 2.15 ( 394) hydrogen bonds : angle 4.68124 / 3.22 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6569 (ttm-80) cc_final: 0.6161 (ttt90) REVERT: A 325 MET cc_start: 0.5311 (ttp) cc_final: 0.4984 (ttt) REVERT: A 331 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: A 677 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6518 (t80) REVERT: A 743 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.7075 (m-10) REVERT: A 751 ASP cc_start: 0.6741 (t70) cc_final: 0.5950 (p0) REVERT: A 777 ASP cc_start: 0.8119 (t70) cc_final: 0.7574 (p0) REVERT: A 847 TYR cc_start: 0.4830 (OUTLIER) cc_final: 0.3679 (m-10) REVERT: B 191 ASP cc_start: 0.9169 (t0) cc_final: 0.8703 (t0) REVERT: B 388 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7708 (ttp-110) REVERT: B 600 LEU cc_start: 0.7277 (mt) cc_final: 0.6917 (tp) outliers start: 37 outliers final: 26 residues processed: 128 average time/residue: 0.0900 time to fit residues: 16.7160 Evaluate side-chains 129 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 569 HIS ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152710 restraints weight = 12830.981| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.06 r_work: 0.3751 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 11272 Z= 0.154 Angle : 0.787 59.190 15285 Z= 0.454 Chirality : 0.041 0.258 1636 Planarity : 0.005 0.093 2004 Dihedral : 5.974 48.137 1565 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.81 % Allowed : 14.92 % Favored : 82.27 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % 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: -0.77 (0.23), residues: 1364 helix: 0.54 (0.26), residues: 458 sheet: -0.78 (0.35), residues: 207 loop : -1.11 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 281 TYR 0.013 0.001 TYR A 811 PHE 0.011 0.001 PHE A 308 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (11266) covalent geometry : angle 0.78738 / 0.45 (15273) SS BOND : bond 0.00213 / 0.11 ( 6) SS BOND : angle 0.59933 / 0.34 ( 12) hydrogen bonds : bond 0.03335 / 2.17 ( 394) hydrogen bonds : angle 4.68026 / 3.22 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6534 (ttm-80) cc_final: 0.6087 (ttt90) REVERT: A 325 MET cc_start: 0.5104 (ttp) cc_final: 0.4801 (ttt) REVERT: A 331 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: A 465 GLU cc_start: 0.8392 (mp0) cc_final: 0.8063 (mt-10) REVERT: A 677 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6503 (t80) REVERT: A 743 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: A 751 ASP cc_start: 0.6683 (t70) cc_final: 0.5844 (p0) REVERT: A 777 ASP cc_start: 0.8073 (t70) cc_final: 0.7497 (p0) REVERT: A 847 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.3577 (m-10) REVERT: B 191 ASP cc_start: 0.9148 (t0) cc_final: 0.8672 (t0) REVERT: B 388 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7664 (ttp-110) REVERT: B 600 LEU cc_start: 0.7286 (mt) cc_final: 0.6902 (tp) outliers start: 33 outliers final: 27 residues processed: 119 average time/residue: 0.0911 time to fit residues: 16.0917 Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 847 TYR Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 680 TYR Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 756 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 115 optimal weight: 0.0060 chunk 113 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 HIS ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.152600 restraints weight = 12847.028| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.08 r_work: 0.3750 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 11272 Z= 0.154 Angle : 0.787 59.190 15285 Z= 0.454 Chirality : 0.041 0.258 1636 Planarity : 0.005 0.093 2004 Dihedral : 5.974 48.137 1565 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.73 % Allowed : 14.92 % Favored : 82.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % 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: -0.77 (0.23), residues: 1364 helix: 0.54 (0.26), residues: 458 sheet: -0.78 (0.35), residues: 207 loop : -1.11 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 281 TYR 0.013 0.001 TYR A 811 PHE 0.011 0.001 PHE A 308 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (11266) covalent geometry : angle 0.78738 / 0.45 (15273) SS BOND : bond 0.00213 / 0.11 ( 6) SS BOND : angle 0.59933 / 0.34 ( 12) hydrogen bonds : bond 0.03335 / 2.17 ( 394) hydrogen bonds : angle 4.68026 / 3.22 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.73 seconds wall clock time: 38 minutes 18.38 seconds (2298.38 seconds total)