Starting phenix.real_space_refine on Sun Apr 5 15:01:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o4g_70100/04_2026/9o4g_70100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o4g_70100/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9o4g_70100/04_2026/9o4g_70100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o4g_70100/04_2026/9o4g_70100.map" model { file = "/net/cci-nas-00/data/ceres_data/9o4g_70100/04_2026/9o4g_70100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o4g_70100/04_2026/9o4g_70100.cif" } 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-2.1rc1-6017/lib/python3.9/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, 27 Unusual residues: {' MN': 2, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.54, per 1000 atoms: 0.23 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: 0.87 Conformation dependent library (CDL) restraints added in 512.6 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: 1.96 Time building geometry restraints manager: 1.18 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 2.320 nonbonded pdb=" OD2 ASP A 263 " pdb="MN MN A 901 " model vdw 2.232 2.320 nonbonded pdb=" NE2 HIS A 394 " pdb="MN MN A 901 " model vdw 2.276 2.400 nonbonded pdb=" NE2 HIS A 831 " pdb="MN MN A 902 " model vdw 2.331 2.400 nonbonded pdb="MN MN A 901 " pdb=" O2A UDP A 903 " model vdw 2.356 2.320 ... (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: 1.180 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 covalent geometry : bond 0.00345 (11266) covalent geometry : angle 0.60731 (15273) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.70383 ( 12) hydrogen bonds : bond 0.20154 ( 394) hydrogen bonds : angle 7.86579 ( 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 : 0.433 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: 0.1255 time to fit residues: 21.4261 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 : 0.364 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4412 r_free = 0.4412 target = 0.201553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158950 restraints weight = 12714.106| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.98 r_work: 0.3801 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11272 Z= 0.145 Angle : 0.538 8.072 15285 Z= 0.279 Chirality : 0.042 0.144 1636 Planarity : 0.005 0.055 2004 Dihedral : 7.045 56.522 1591 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.64 % Allowed : 11.25 % Favored : 86.10 % 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: -0.96 (0.22), residues: 1364 helix: -0.06 (0.25), residues: 467 sheet: -0.55 (0.36), residues: 208 loop : -1.01 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 483 TYR 0.018 0.001 TYR A 743 PHE 0.018 0.001 PHE A 468 TRP 0.013 0.002 TRP A 359 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00341 (11266) covalent geometry : angle 0.53784 (15273) SS BOND : bond 0.00159 ( 6) SS BOND : angle 0.72236 ( 12) hydrogen bonds : bond 0.04874 ( 394) hydrogen bonds : angle 5.67288 ( 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 152 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7509 (ttm) REVERT: A 325 MET cc_start: 0.5208 (ttp) cc_final: 0.4915 (ttt) REVERT: A 331 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: A 438 GLU cc_start: 0.7026 (pm20) cc_final: 0.6595 (pm20) REVERT: A 675 LYS cc_start: 0.7543 (mttt) cc_final: 0.6952 (mmtt) REVERT: A 685 GLU cc_start: 0.6195 (mp0) cc_final: 0.5642 (mp0) REVERT: A 751 ASP cc_start: 0.7248 (t70) cc_final: 0.6300 (p0) REVERT: A 777 ASP cc_start: 0.8139 (t70) cc_final: 0.7575 (p0) REVERT: A 847 TYR cc_start: 0.4829 (OUTLIER) cc_final: 0.3582 (m-10) REVERT: B 191 ASP cc_start: 0.9160 (t0) cc_final: 0.8792 (t0) REVERT: B 262 HIS cc_start: 0.7027 (m-70) cc_final: 0.6740 (m-70) REVERT: B 349 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.5864 (t80) REVERT: B 419 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7708 (tpt90) REVERT: B 645 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7291 (tm-30) outliers start: 31 outliers final: 20 residues processed: 140 average time/residue: 0.1211 time to fit residues: 23.7871 Evaluate side-chains 137 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 829 VAL 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 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: 3.9990 chunk 105 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4448 r_free = 0.4448 target = 0.205463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163743 restraints weight = 12672.336| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.03 r_work: 0.3931 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11272 Z= 0.092 Angle : 0.466 6.148 15285 Z= 0.240 Chirality : 0.040 0.143 1636 Planarity : 0.004 0.055 2004 Dihedral : 6.268 59.083 1575 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.73 % Allowed : 11.59 % Favored : 85.68 % 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: -0.73 (0.23), residues: 1364 helix: 0.25 (0.25), residues: 468 sheet: -0.59 (0.36), residues: 201 loop : -0.90 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 483 TYR 0.021 0.001 TYR A 743 PHE 0.009 0.001 PHE A 468 TRP 0.009 0.001 TRP B 357 HIS 0.003 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00197 (11266) covalent geometry : angle 0.46578 (15273) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.61295 ( 12) hydrogen bonds : bond 0.03633 ( 394) hydrogen bonds : angle 5.04920 ( 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: 32 poor density : 117 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7399 (ttm) REVERT: A 325 MET cc_start: 0.5074 (ttp) cc_final: 0.4829 (ttt) REVERT: A 331 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: A 675 LYS cc_start: 0.7624 (mttt) cc_final: 0.7051 (mmtt) REVERT: A 685 GLU cc_start: 0.6114 (mp0) cc_final: 0.5656 (mp0) REVERT: A 751 ASP cc_start: 0.6986 (t70) cc_final: 0.6071 (p0) REVERT: A 777 ASP cc_start: 0.8048 (t70) cc_final: 0.7507 (p0) REVERT: A 847 TYR cc_start: 0.4803 (OUTLIER) cc_final: 0.3539 (m-10) REVERT: B 191 ASP cc_start: 0.9121 (t0) cc_final: 0.8720 (t0) REVERT: B 262 HIS cc_start: 0.6982 (m-70) cc_final: 0.6708 (m-70) REVERT: B 419 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7126 (tpt-90) REVERT: B 600 LEU cc_start: 0.6985 (mt) cc_final: 0.6730 (tp) REVERT: B 645 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7206 (tm-30) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 0.1109 time to fit residues: 22.2430 Evaluate side-chains 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 298 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 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: 0.4980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4422 r_free = 0.4422 target = 0.202691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.160634 restraints weight = 12767.795| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.04 r_work: 0.3915 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11272 Z= 0.125 Angle : 0.487 6.107 15285 Z= 0.251 Chirality : 0.041 0.152 1636 Planarity : 0.004 0.055 2004 Dihedral : 6.299 55.153 1573 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.90 % Allowed : 12.53 % Favored : 84.57 % 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: -0.76 (0.23), residues: 1364 helix: 0.30 (0.25), residues: 465 sheet: -0.62 (0.36), residues: 206 loop : -0.98 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 460 TYR 0.022 0.001 TYR A 743 PHE 0.017 0.001 PHE A 695 TRP 0.011 0.001 TRP A 359 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00300 (11266) covalent geometry : angle 0.48703 (15273) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.60500 ( 12) hydrogen bonds : bond 0.03806 ( 394) hydrogen bonds : angle 4.97970 ( 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: 34 poor density : 106 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 310 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7436 (ttm) REVERT: A 331 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: A 469 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 675 LYS cc_start: 0.7659 (mttt) cc_final: 0.7070 (mmtt) REVERT: A 685 GLU cc_start: 0.6206 (mp0) cc_final: 0.5682 (mp0) REVERT: A 751 ASP cc_start: 0.7034 (t70) cc_final: 0.6112 (p0) REVERT: A 777 ASP cc_start: 0.8156 (t70) cc_final: 0.7591 (p0) REVERT: A 847 TYR cc_start: 0.4906 (OUTLIER) cc_final: 0.3761 (m-10) REVERT: B 191 ASP cc_start: 0.9107 (t0) cc_final: 0.8712 (t0) REVERT: B 262 HIS cc_start: 0.7039 (m-70) cc_final: 0.6789 (m-70) REVERT: B 600 LEU cc_start: 0.7314 (mt) cc_final: 0.6984 (tp) outliers start: 34 outliers final: 24 residues processed: 129 average time/residue: 0.1129 time to fit residues: 20.9012 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 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 718 ASP 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 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 756 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 28 optimal weight: 0.7980 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: 0.6980 chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 0.0670 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 507 ASN B 569 HIS B 718 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.205437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.163714 restraints weight = 12683.915| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.99 r_work: 0.3851 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11272 Z= 0.135 Angle : 0.505 6.394 15285 Z= 0.260 Chirality : 0.042 0.151 1636 Planarity : 0.004 0.053 2004 Dihedral : 6.251 50.745 1569 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.32 % Allowed : 13.13 % Favored : 83.55 % 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: -0.83 (0.23), residues: 1364 helix: 0.27 (0.25), residues: 463 sheet: -0.65 (0.36), residues: 206 loop : -1.04 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 388 TYR 0.028 0.002 TYR A 743 PHE 0.019 0.001 PHE A 695 TRP 0.012 0.001 TRP A 359 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00325 (11266) covalent geometry : angle 0.50482 (15273) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.64598 ( 12) hydrogen bonds : bond 0.03915 ( 394) hydrogen bonds : angle 4.96637 ( 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 150 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.396 Fit side-chains REVERT: A 306 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7246 (mp0) REVERT: A 310 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7396 (ttm) REVERT: A 331 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: A 469 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8098 (pp) REVERT: A 646 LEU cc_start: 0.6332 (mt) cc_final: 0.6130 (mp) REVERT: A 675 LYS cc_start: 0.7650 (mttt) cc_final: 0.6994 (mmtt) REVERT: A 685 GLU cc_start: 0.6319 (mp0) cc_final: 0.5777 (mp0) REVERT: A 751 ASP cc_start: 0.7049 (t70) cc_final: 0.6086 (p0) REVERT: A 777 ASP cc_start: 0.8266 (t70) cc_final: 0.7644 (p0) REVERT: A 847 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.3693 (m-10) REVERT: B 191 ASP cc_start: 0.9154 (t0) cc_final: 0.8703 (t0) REVERT: B 262 HIS cc_start: 0.7060 (m-70) cc_final: 0.6783 (m-70) REVERT: B 600 LEU cc_start: 0.7319 (mt) cc_final: 0.6994 (tp) REVERT: B 645 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7159 (tm-30) outliers start: 39 outliers final: 27 residues processed: 140 average time/residue: 0.0999 time to fit residues: 20.5298 Evaluate side-chains 131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 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 718 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 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 756 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 52 optimal weight: 0.0030 chunk 72 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4508 r_free = 0.4508 target = 0.209318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.167799 restraints weight = 12749.503| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.91 r_work: 0.3959 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11272 Z= 0.087 Angle : 0.466 8.986 15285 Z= 0.235 Chirality : 0.040 0.150 1636 Planarity : 0.004 0.054 2004 Dihedral : 5.934 48.412 1569 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.39 % Allowed : 14.24 % Favored : 83.38 % 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: -0.63 (0.23), residues: 1364 helix: 0.52 (0.26), residues: 465 sheet: -0.64 (0.36), residues: 201 loop : -0.95 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 388 TYR 0.021 0.001 TYR A 743 PHE 0.016 0.001 PHE A 695 TRP 0.009 0.001 TRP B 357 HIS 0.003 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00192 (11266) covalent geometry : angle 0.46589 (15273) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.56513 ( 12) hydrogen bonds : bond 0.03188 ( 394) hydrogen bonds : angle 4.69663 ( 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 134 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7971 (tp30) cc_final: 0.7465 (mt-10) REVERT: A 646 LEU cc_start: 0.6355 (mt) cc_final: 0.6137 (mp) REVERT: A 675 LYS cc_start: 0.7647 (mttt) cc_final: 0.7002 (mmtt) REVERT: A 685 GLU cc_start: 0.6173 (mp0) cc_final: 0.5708 (mp0) REVERT: A 743 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: A 751 ASP cc_start: 0.6738 (t70) cc_final: 0.6059 (p0) REVERT: A 777 ASP cc_start: 0.8153 (t70) cc_final: 0.7654 (p0) REVERT: A 847 TYR cc_start: 0.4982 (OUTLIER) cc_final: 0.3757 (m-10) REVERT: B 191 ASP cc_start: 0.9151 (t0) cc_final: 0.8675 (t0) REVERT: B 262 HIS cc_start: 0.7054 (m-70) cc_final: 0.6792 (m-70) REVERT: B 600 LEU cc_start: 0.7294 (mt) cc_final: 0.6888 (tp) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.0996 time to fit residues: 18.6560 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 307 ASN 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 635 LEU Chi-restraints excluded: chain A residue 677 TYR Chi-restraints excluded: chain A residue 718 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 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 756 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 121 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4491 r_free = 0.4491 target = 0.207238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165709 restraints weight = 12657.811| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.03 r_work: 0.3846 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1574 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= 0.116 Angle : 0.482 8.231 15285 Z= 0.244 Chirality : 0.041 0.154 1636 Planarity : 0.004 0.054 2004 Dihedral : 5.847 46.465 1564 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.39 % Allowed : 14.83 % Favored : 82.78 % 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: -0.65 (0.23), residues: 1364 helix: 0.50 (0.26), residues: 463 sheet: -0.57 (0.36), residues: 206 loop : -0.99 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.022 0.001 TYR A 743 PHE 0.019 0.001 PHE A 695 TRP 0.010 0.001 TRP A 359 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00278 (11266) covalent geometry : angle 0.48169 (15273) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.55511 ( 12) hydrogen bonds : bond 0.03477 ( 394) hydrogen bonds : angle 4.74442 ( 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 131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 202 ARG cc_start: 0.6530 (ttm-80) cc_final: 0.6145 (ttt90) REVERT: A 331 GLU cc_start: 0.7950 (tp30) cc_final: 0.7445 (mt-10) REVERT: A 675 LYS cc_start: 0.7595 (mttt) cc_final: 0.6953 (mmtt) REVERT: A 677 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 685 GLU cc_start: 0.6120 (mp0) cc_final: 0.5678 (mp0) REVERT: A 743 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: A 751 ASP cc_start: 0.6758 (t70) cc_final: 0.6033 (p0) REVERT: A 777 ASP cc_start: 0.8136 (t70) cc_final: 0.7707 (p0) REVERT: A 847 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.3676 (m-10) REVERT: B 191 ASP cc_start: 0.9177 (t0) cc_final: 0.8713 (t0) REVERT: B 262 HIS cc_start: 0.7052 (m-70) cc_final: 0.6794 (m-70) REVERT: B 600 LEU cc_start: 0.7307 (mt) cc_final: 0.6892 (tp) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.1096 time to fit residues: 19.5933 Evaluate side-chains 124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 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 291 LEU Chi-restraints excluded: chain A residue 349 VAL 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 718 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 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 712 LEU Chi-restraints excluded: chain B residue 715 SER 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: 0.8980 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4502 r_free = 0.4502 target = 0.208520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167132 restraints weight = 12718.350| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.89 r_work: 0.3886 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1717 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= 0.097 Angle : 0.467 7.862 15285 Z= 0.235 Chirality : 0.040 0.152 1636 Planarity : 0.004 0.053 2004 Dihedral : 5.725 46.568 1564 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.90 % Allowed : 14.32 % Favored : 82.78 % 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: -0.56 (0.23), residues: 1364 helix: 0.66 (0.26), residues: 459 sheet: -0.60 (0.36), residues: 201 loop : -0.97 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 388 TYR 0.017 0.001 TYR A 743 PHE 0.019 0.001 PHE A 695 TRP 0.010 0.001 TRP B 357 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00228 (11266) covalent geometry : angle 0.46693 (15273) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.58339 ( 12) hydrogen bonds : bond 0.03231 ( 394) hydrogen bonds : angle 4.61897 ( 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 139 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.405 Fit side-chains REVERT: A 202 ARG cc_start: 0.6503 (ttm-80) cc_final: 0.6149 (ttt90) REVERT: A 310 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7422 (ttm) REVERT: A 331 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: A 677 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 685 GLU cc_start: 0.6187 (mp0) cc_final: 0.5774 (mp0) REVERT: A 743 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: A 751 ASP cc_start: 0.6701 (t70) cc_final: 0.5956 (p0) REVERT: A 777 ASP cc_start: 0.8100 (t70) cc_final: 0.7629 (p0) REVERT: A 847 TYR cc_start: 0.4857 (OUTLIER) cc_final: 0.3675 (m-10) REVERT: B 191 ASP cc_start: 0.9161 (t0) cc_final: 0.8681 (t0) REVERT: B 262 HIS cc_start: 0.7009 (m-70) cc_final: 0.6738 (m-70) REVERT: B 600 LEU cc_start: 0.7315 (mt) cc_final: 0.6927 (tp) outliers start: 34 outliers final: 25 residues processed: 128 average time/residue: 0.1055 time to fit residues: 19.4639 Evaluate side-chains 128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 310 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 402 GLN 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 718 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 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 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: 2.9990 chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4483 r_free = 0.4483 target = 0.206230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.163934 restraints weight = 12691.358| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.05 r_work: 0.3830 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11272 Z= 0.135 Angle : 0.507 7.469 15285 Z= 0.256 Chirality : 0.042 0.159 1636 Planarity : 0.004 0.054 2004 Dihedral : 5.909 47.492 1564 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.07 % Allowed : 14.41 % Favored : 82.52 % 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: -0.69 (0.23), residues: 1364 helix: 0.58 (0.26), residues: 456 sheet: -0.59 (0.37), residues: 206 loop : -1.08 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 507 TYR 0.020 0.001 TYR A 743 PHE 0.021 0.001 PHE A 695 TRP 0.011 0.001 TRP A 359 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00328 (11266) covalent geometry : angle 0.50679 (15273) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.65501 ( 12) hydrogen bonds : bond 0.03602 ( 394) hydrogen bonds : angle 4.73702 ( 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 131 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.487 Fit side-chains REVERT: A 202 ARG cc_start: 0.6578 (ttm-80) cc_final: 0.6202 (ttt90) REVERT: A 303 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 306 GLU cc_start: 0.7408 (mp0) cc_final: 0.7184 (mp0) REVERT: A 331 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: A 677 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.6199 (t80) REVERT: A 685 GLU cc_start: 0.6163 (mp0) cc_final: 0.5745 (mp0) REVERT: A 743 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: A 751 ASP cc_start: 0.6827 (t70) cc_final: 0.6581 (t70) REVERT: A 777 ASP cc_start: 0.8167 (t70) cc_final: 0.7728 (p0) REVERT: A 847 TYR cc_start: 0.4879 (OUTLIER) cc_final: 0.3691 (m-10) REVERT: B 191 ASP cc_start: 0.9178 (t0) cc_final: 0.8729 (t0) REVERT: B 262 HIS cc_start: 0.7070 (m-70) cc_final: 0.6814 (m-70) REVERT: B 600 LEU cc_start: 0.7302 (mt) cc_final: 0.6910 (tp) outliers start: 36 outliers final: 28 residues processed: 121 average time/residue: 0.1014 time to fit residues: 18.2469 Evaluate side-chains 123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 307 ASN Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 349 VAL 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 718 ASP Chi-restraints excluded: chain A residue 726 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 137 VAL 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 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 712 LEU 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: 0.1980 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4492 r_free = 0.4492 target = 0.207251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.164784 restraints weight = 12727.247| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.06 r_work: 0.3907 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11272 Z= 0.112 Angle : 0.490 7.498 15285 Z= 0.247 Chirality : 0.041 0.159 1636 Planarity : 0.004 0.053 2004 Dihedral : 5.849 48.083 1564 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.98 % Allowed : 14.75 % Favored : 82.27 % 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: -0.67 (0.23), residues: 1364 helix: 0.63 (0.26), residues: 456 sheet: -0.58 (0.37), residues: 206 loop : -1.10 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 507 TYR 0.019 0.001 TYR A 743 PHE 0.021 0.001 PHE A 695 TRP 0.011 0.001 TRP B 357 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00267 (11266) covalent geometry : angle 0.48974 (15273) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.62641 ( 12) hydrogen bonds : bond 0.03434 ( 394) hydrogen bonds : angle 4.68730 ( 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 132 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.357 Fit side-chains REVERT: A 202 ARG cc_start: 0.6547 (ttm-80) cc_final: 0.6171 (ttt90) REVERT: A 303 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 306 GLU cc_start: 0.7506 (mp0) cc_final: 0.7241 (mp0) REVERT: A 331 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: A 677 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6332 (t80) REVERT: A 685 GLU cc_start: 0.6196 (mp0) cc_final: 0.5771 (mp0) REVERT: A 743 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: A 751 ASP cc_start: 0.6804 (t70) cc_final: 0.6555 (t70) REVERT: A 777 ASP cc_start: 0.8173 (t70) cc_final: 0.7752 (p0) REVERT: A 847 TYR cc_start: 0.4881 (OUTLIER) cc_final: 0.3686 (m-10) REVERT: B 191 ASP cc_start: 0.9171 (t0) cc_final: 0.8708 (t0) REVERT: B 262 HIS cc_start: 0.7060 (m-70) cc_final: 0.6801 (m-70) REVERT: B 600 LEU cc_start: 0.7277 (mt) cc_final: 0.6893 (tp) outliers start: 35 outliers final: 28 residues processed: 122 average time/residue: 0.1009 time to fit residues: 18.3147 Evaluate side-chains 127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 291 LEU 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 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 718 ASP Chi-restraints excluded: chain A residue 726 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 137 VAL 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 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 712 LEU 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: 0.0670 chunk 4 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4488 r_free = 0.4488 target = 0.206746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.164386 restraints weight = 12761.227| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.07 r_work: 0.3912 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1844 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= 0.119 Angle : 0.494 7.328 15285 Z= 0.250 Chirality : 0.041 0.157 1636 Planarity : 0.004 0.053 2004 Dihedral : 5.863 48.595 1564 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.24 % Allowed : 14.66 % 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: -0.68 (0.23), residues: 1364 helix: 0.63 (0.26), residues: 455 sheet: -0.58 (0.37), residues: 206 loop : -1.13 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 507 TYR 0.018 0.001 TYR A 743 PHE 0.021 0.001 PHE A 695 TRP 0.011 0.001 TRP B 357 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00286 (11266) covalent geometry : angle 0.49360 (15273) SS BOND : bond 0.00174 ( 6) SS BOND : angle 0.56660 ( 12) hydrogen bonds : bond 0.03509 ( 394) hydrogen bonds : angle 4.69631 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.88 seconds wall clock time: 44 minutes 12.43 seconds (2652.43 seconds total)