Starting phenix.real_space_refine on Thu Aug 6 02:37:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.cif Found real_map, /net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10et_75118/08_2026/10et_75118.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8049 2.51 5 N 2168 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12659 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6366 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 57, 'TRANS': 749} Chain: "A" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6293 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.21 Number of scatterers: 12659 At special positions: 0 Unit cell: (102.75, 163.03, 101.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2400 8.00 N 2168 7.00 C 8049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 447.0 milliseconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2986 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 24 sheets defined 16.3% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.928A pdb=" N LEU B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 removed outlier: 3.557A pdb=" N SER B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 645 through 649 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.985A pdb=" N GLY B 702 " --> pdb=" O LYS B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 724 Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.617A pdb=" N VAL B 754 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 794 removed outlier: 4.271A pdb=" N PHE B 785 " --> pdb=" O SER B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 833 removed outlier: 3.562A pdb=" N TYR B 831 " --> pdb=" O ALA B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 835 No H-bonds generated for 'chain 'B' and resid 834 through 835' Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.847A pdb=" N SER B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 911 removed outlier: 3.742A pdb=" N LEU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP B 902 " --> pdb=" O MET B 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.823A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.821A pdb=" N ASP A 151 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.596A pdb=" N ARG A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 378 " --> pdb=" O CYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 768 removed outlier: 3.964A pdb=" N ALA A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 823 through 826 Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.853A pdb=" N TYR A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.702A pdb=" N ALA A 840 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 874 removed outlier: 3.993A pdb=" N PHE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 912 removed outlier: 3.548A pdb=" N ILE A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.841A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 210 removed outlier: 4.215A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 264 through 267 removed outlier: 6.644A pdb=" N THR B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 271 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 333 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 344 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 330 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 294 through 297 removed outlier: 6.543A pdb=" N ILE A 847 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL A 882 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 849 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 884 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS A 851 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 848 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS A 800 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE A 775 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N ILE A 802 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 777 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ARG A 804 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY A 779 " --> pdb=" O ARG A 804 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N LEU A 684 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS A 774 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 353 removed outlier: 7.041A pdb=" N VAL B 382 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 393 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR B 386 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE B 391 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 416 through 420 removed outlier: 5.958A pdb=" N SER B 417 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA B 431 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 419 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 429 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 447 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 467 " --> pdb=" O ASP B 447 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 449 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 471 through 479 removed outlier: 6.745A pdb=" N TYR B 486 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 475 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU B 484 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TRP B 477 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU B 482 " --> pdb=" O TRP B 477 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL B 499 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE B 511 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.715A pdb=" N GLY B 556 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU B 583 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 568 " --> pdb=" O ILE B 581 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.788A pdb=" N TYR B 551 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AB3, first strand: chain 'B' and resid 590 through 596 removed outlier: 4.960A pdb=" N GLU B 591 " --> pdb=" O GLU B 617 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU B 617 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 593 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 615 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 595 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 652 through 659 removed outlier: 3.534A pdb=" N GLN B 652 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 672 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP B 689 " --> pdb=" O LEU B 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AB6, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AB7, first strand: chain 'A' and resid 220 through 222 Processing sheet with id=AB8, first strand: chain 'A' and resid 270 through 275 removed outlier: 3.553A pdb=" N ALA A 333 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 348 through 353 removed outlier: 6.595A pdb=" N SER A 363 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 351 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 361 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR A 359 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS A 396 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR A 386 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 392 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.951A pdb=" N VAL A 449 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 465 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 470 through 475 removed outlier: 3.590A pdb=" N LEU A 470 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 486 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY A 474 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 484 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 500 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.825A pdb=" N SER A 526 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A 555 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 570 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG A 580 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.825A pdb=" N SER A 526 " --> pdb=" O ASN A 555 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A 555 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 551 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AC6, first strand: chain 'A' and resid 590 through 596 removed outlier: 5.440A pdb=" N GLU A 591 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU A 617 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 593 " --> pdb=" O SER A 615 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 615 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 595 " --> pdb=" O LEU A 613 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4162 1.34 - 1.46: 2554 1.46 - 1.57: 6200 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 12984 Sorted by residual: bond pdb=" CB ASN B 819 " pdb=" CG ASN B 819 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" C ARG B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.41e-01 bond pdb=" CA ASN B 819 " pdb=" CB ASN B 819 " ideal model delta sigma weight residual 1.532 1.543 -0.011 1.43e-02 4.89e+03 5.56e-01 bond pdb=" C TRP B 630 " pdb=" N PRO B 631 " ideal model delta sigma weight residual 1.334 1.345 -0.011 1.51e-02 4.39e+03 5.36e-01 bond pdb=" CA VAL A 913 " pdb=" C VAL A 913 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.05e-02 9.07e+03 5.13e-01 ... (remaining 12979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 17090 1.23 - 2.45: 440 2.45 - 3.68: 110 3.68 - 4.90: 16 4.90 - 6.13: 5 Bond angle restraints: 17661 Sorted by residual: angle pdb=" N VAL B 764 " pdb=" CA VAL B 764 " pdb=" C VAL B 764 " ideal model delta sigma weight residual 112.98 109.18 3.80 1.25e+00 6.40e-01 9.23e+00 angle pdb=" C GLN B 818 " pdb=" N ASN B 819 " pdb=" CA ASN B 819 " ideal model delta sigma weight residual 124.31 128.85 -4.54 1.67e+00 3.59e-01 7.39e+00 angle pdb=" N TRP B 630 " pdb=" CA TRP B 630 " pdb=" C TRP B 630 " ideal model delta sigma weight residual 109.81 114.94 -5.13 2.21e+00 2.05e-01 5.39e+00 angle pdb=" N VAL A 913 " pdb=" CA VAL A 913 " pdb=" C VAL A 913 " ideal model delta sigma weight residual 108.88 113.60 -4.72 2.16e+00 2.14e-01 4.77e+00 angle pdb=" CA ASN B 819 " pdb=" CB ASN B 819 " pdb=" CG ASN B 819 " ideal model delta sigma weight residual 112.60 114.78 -2.18 1.00e+00 1.00e+00 4.76e+00 ... (remaining 17656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 7029 16.41 - 32.81: 633 32.81 - 49.22: 123 49.22 - 65.63: 17 65.63 - 82.03: 17 Dihedral angle restraints: 7819 sinusoidal: 3172 harmonic: 4647 Sorted by residual: dihedral pdb=" CA HIS B 366 " pdb=" C HIS B 366 " pdb=" N ARG B 367 " pdb=" CA ARG B 367 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA TYR A 749 " pdb=" C TYR A 749 " pdb=" N VAL A 750 " pdb=" CA VAL A 750 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA TYR A 325 " pdb=" C TYR A 325 " pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta harmonic sigma weight residual -180.00 -164.44 -15.56 0 5.00e+00 4.00e-02 9.68e+00 ... (remaining 7816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1250 0.033 - 0.067: 460 0.067 - 0.100: 132 0.100 - 0.133: 82 0.133 - 0.166: 2 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA ASN B 819 " pdb=" N ASN B 819 " pdb=" C ASN B 819 " pdb=" CB ASN B 819 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA TRP A 630 " pdb=" N TRP A 630 " pdb=" C TRP A 630 " pdb=" CB TRP A 630 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1923 not shown) Planarity restraints: 2302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 113 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 114 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 444 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 445 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 246 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO B 247 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.025 5.00e-02 4.00e+02 ... (remaining 2299 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 370 2.71 - 3.26: 11563 3.26 - 3.81: 18309 3.81 - 4.35: 22462 4.35 - 4.90: 40293 Nonbonded interactions: 92997 Sorted by model distance: nonbonded pdb=" OD1 ASP B 479 " pdb=" N ASP B 480 " model vdw 2.167 3.120 nonbonded pdb=" OG SER B 251 " pdb=" OD1 ASP B 253 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR B 676 " pdb=" O GLY B 682 " model vdw 2.219 3.040 nonbonded pdb=" ND2 ASN A 746 " pdb=" OE1 GLU A 820 " model vdw 2.227 3.120 nonbonded pdb=" O GLY B 189 " pdb=" NE2 GLN B 636 " model vdw 2.244 3.120 ... (remaining 92992 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 108 through 695 or resid 706 through 915)) } 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: 0.570 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.200 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.002 0.031 12984 Z= 0.108 Angle : 0.516 6.131 17661 Z= 0.273 Chirality : 0.042 0.166 1926 Planarity : 0.005 0.053 2302 Dihedral : 13.179 82.034 4833 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1598 helix: -0.27 (0.39), residues: 190 sheet: 0.32 (0.26), residues: 433 loop : -1.26 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 515 TYR 0.015 0.001 TYR A 645 PHE 0.015 0.001 PHE B 817 TRP 0.012 0.001 TRP A 722 HIS 0.008 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (12984) covalent geometry : angle 0.51587 / 0.27 (17661) hydrogen bonds : bond 0.18226 / 11.57 ( 360) hydrogen bonds : angle 7.32353 / 5.18 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.410 Fit side-chains REVERT: B 645 TYR cc_start: 0.8222 (p90) cc_final: 0.7984 (p90) REVERT: B 898 MET cc_start: 0.7606 (tpp) cc_final: 0.7056 (tpp) REVERT: A 374 PRO cc_start: 0.7341 (Cg_exo) cc_final: 0.6967 (Cg_endo) REVERT: A 415 MET cc_start: 0.4783 (mtt) cc_final: 0.4439 (mmm) REVERT: A 419 ASN cc_start: 0.7278 (m110) cc_final: 0.6917 (m110) REVERT: A 494 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7482 (mtp-110) REVERT: A 554 LEU cc_start: 0.7623 (pp) cc_final: 0.7101 (mp) outliers start: 0 outliers final: 1 residues processed: 258 average time/residue: 0.4820 time to fit residues: 136.1153 Evaluate side-chains 125 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN B 366 HIS B 628 GLN B 780 HIS B 829 ASN B 899 HIS A 643 HIS A 665 GLN A 780 HIS ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS A 909 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117063 restraints weight = 17921.444| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.18 r_work: 0.3320 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12984 Z= 0.150 Angle : 0.605 8.651 17661 Z= 0.314 Chirality : 0.045 0.165 1926 Planarity : 0.005 0.059 2302 Dihedral : 4.121 14.223 1756 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.52 % Allowed : 10.37 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1598 helix: 0.38 (0.39), residues: 194 sheet: 0.29 (0.26), residues: 410 loop : -1.28 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 515 TYR 0.022 0.001 TYR A 521 PHE 0.018 0.002 PHE A 513 TRP 0.021 0.001 TRP A 630 HIS 0.006 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (12984) covalent geometry : angle 0.60459 / 0.31 (17661) hydrogen bonds : bond 0.05288 / 3.62 ( 360) hydrogen bonds : angle 5.43294 / 3.83 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: B 661 LYS cc_start: 0.8459 (tppp) cc_final: 0.8078 (tptm) REVERT: B 740 GLU cc_start: 0.6331 (tt0) cc_final: 0.5635 (pp20) REVERT: B 744 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6637 (tp30) REVERT: B 762 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6992 (tm-30) REVERT: B 898 MET cc_start: 0.7708 (tpp) cc_final: 0.7331 (tpp) REVERT: A 186 LEU cc_start: 0.6311 (mt) cc_final: 0.5823 (tm) REVERT: A 374 PRO cc_start: 0.7255 (Cg_exo) cc_final: 0.7000 (Cg_endo) REVERT: A 402 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 419 ASN cc_start: 0.7216 (m110) cc_final: 0.6808 (m110) REVERT: A 449 VAL cc_start: 0.7889 (m) cc_final: 0.7650 (m) REVERT: A 461 GLU cc_start: 0.7599 (pm20) cc_final: 0.7312 (pm20) REVERT: A 493 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7505 (mmt90) REVERT: A 494 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.6965 (mtp180) REVERT: A 514 ASP cc_start: 0.8456 (p0) cc_final: 0.7931 (p0) REVERT: A 554 LEU cc_start: 0.6840 (pp) cc_final: 0.6283 (mp) REVERT: A 581 ILE cc_start: 0.8447 (mm) cc_final: 0.8213 (mp) REVERT: A 863 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5597 (ptm) outliers start: 35 outliers final: 17 residues processed: 158 average time/residue: 0.4530 time to fit residues: 79.3573 Evaluate side-chains 138 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 863 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN A 752 GLN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112815 restraints weight = 18135.785| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.21 r_work: 0.3271 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12984 Z= 0.201 Angle : 0.633 7.217 17661 Z= 0.331 Chirality : 0.046 0.171 1926 Planarity : 0.005 0.064 2302 Dihedral : 4.391 16.949 1754 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.88 % Allowed : 13.17 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1598 helix: 0.10 (0.37), residues: 199 sheet: 0.01 (0.26), residues: 412 loop : -1.43 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 515 TYR 0.023 0.002 TYR B 676 PHE 0.018 0.002 PHE A 513 TRP 0.019 0.002 TRP A 630 HIS 0.011 0.002 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (12984) covalent geometry : angle 0.63344 / 0.33 (17661) hydrogen bonds : bond 0.05575 / 3.81 ( 360) hydrogen bonds : angle 5.37173 / 3.77 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.385 Fit side-chains REVERT: B 505 ASN cc_start: 0.7311 (p0) cc_final: 0.6267 (t0) REVERT: B 740 GLU cc_start: 0.6366 (tt0) cc_final: 0.5621 (pp20) REVERT: B 744 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6604 (tp30) REVERT: B 762 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6861 (tm-30) REVERT: B 898 MET cc_start: 0.7794 (tpp) cc_final: 0.7571 (mmt) REVERT: A 391 PHE cc_start: 0.8095 (t80) cc_final: 0.7456 (t80) REVERT: A 402 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 415 MET cc_start: 0.3670 (mtp) cc_final: 0.2398 (mmm) REVERT: A 419 ASN cc_start: 0.7267 (m110) cc_final: 0.6865 (m110) REVERT: A 441 MET cc_start: 0.5137 (pp-130) cc_final: 0.4879 (pp-130) REVERT: A 461 GLU cc_start: 0.7606 (pm20) cc_final: 0.7222 (pm20) REVERT: A 493 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7553 (mmt90) REVERT: A 494 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7016 (mtp180) REVERT: A 514 ASP cc_start: 0.8501 (p0) cc_final: 0.8069 (p0) REVERT: A 581 ILE cc_start: 0.8320 (mm) cc_final: 0.8040 (mp) outliers start: 40 outliers final: 22 residues processed: 156 average time/residue: 0.4987 time to fit residues: 86.3874 Evaluate side-chains 142 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.0570 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 636 GLN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.115127 restraints weight = 18003.685| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.18 r_work: 0.3294 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12984 Z= 0.130 Angle : 0.572 8.667 17661 Z= 0.294 Chirality : 0.043 0.173 1926 Planarity : 0.005 0.061 2302 Dihedral : 4.190 18.248 1754 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.30 % Allowed : 13.97 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1598 helix: 0.40 (0.38), residues: 195 sheet: 0.05 (0.26), residues: 416 loop : -1.36 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 163 TYR 0.023 0.001 TYR B 676 PHE 0.020 0.001 PHE A 513 TRP 0.018 0.001 TRP A 630 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12984) covalent geometry : angle 0.57202 / 0.29 (17661) hydrogen bonds : bond 0.04470 / 3.07 ( 360) hydrogen bonds : angle 5.09586 / 3.58 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: B 312 LEU cc_start: 0.8560 (mt) cc_final: 0.8285 (mt) REVERT: B 505 ASN cc_start: 0.7409 (p0) cc_final: 0.6380 (t0) REVERT: B 740 GLU cc_start: 0.6370 (tt0) cc_final: 0.5677 (pp20) REVERT: B 744 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6562 (tp30) REVERT: B 762 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6867 (tm-30) REVERT: B 838 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7611 (mmt) REVERT: B 898 MET cc_start: 0.7852 (tpp) cc_final: 0.7623 (mmt) REVERT: A 186 LEU cc_start: 0.6310 (mt) cc_final: 0.5723 (tm) REVERT: A 383 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: A 391 PHE cc_start: 0.8210 (t80) cc_final: 0.7942 (t80) REVERT: A 402 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 415 MET cc_start: 0.3467 (mtp) cc_final: 0.2274 (mmm) REVERT: A 419 ASN cc_start: 0.7230 (m110) cc_final: 0.6830 (m110) REVERT: A 441 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4808 (pp-130) REVERT: A 461 GLU cc_start: 0.7499 (pm20) cc_final: 0.6967 (pm20) REVERT: A 494 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7238 (mtp-110) REVERT: A 514 ASP cc_start: 0.8520 (p0) cc_final: 0.7598 (t0) REVERT: A 581 ILE cc_start: 0.8310 (mm) cc_final: 0.8018 (mp) REVERT: A 726 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6720 (tpt-90) outliers start: 32 outliers final: 17 residues processed: 149 average time/residue: 0.4950 time to fit residues: 81.6765 Evaluate side-chains 141 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113002 restraints weight = 18110.986| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.18 r_work: 0.3270 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12984 Z= 0.163 Angle : 0.595 7.925 17661 Z= 0.307 Chirality : 0.044 0.174 1926 Planarity : 0.005 0.061 2302 Dihedral : 4.311 20.654 1754 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.17 % Allowed : 14.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1598 helix: 0.38 (0.37), residues: 198 sheet: -0.06 (0.26), residues: 425 loop : -1.43 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.027 0.002 TYR B 676 PHE 0.022 0.002 PHE A 513 TRP 0.015 0.001 TRP A 630 HIS 0.008 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (12984) covalent geometry : angle 0.59511 / 0.31 (17661) hydrogen bonds : bond 0.04890 / 3.36 ( 360) hydrogen bonds : angle 5.12319 / 3.60 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: B 312 LEU cc_start: 0.8577 (mt) cc_final: 0.8311 (mt) REVERT: B 505 ASN cc_start: 0.7473 (p0) cc_final: 0.6457 (t0) REVERT: B 740 GLU cc_start: 0.6436 (tt0) cc_final: 0.5761 (pp20) REVERT: B 744 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6598 (tp30) REVERT: B 762 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6841 (tm-30) REVERT: B 838 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7676 (mmt) REVERT: B 898 MET cc_start: 0.7895 (tpp) cc_final: 0.7686 (mmt) REVERT: A 383 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6290 (tp30) REVERT: A 391 PHE cc_start: 0.8299 (t80) cc_final: 0.8021 (t80) REVERT: A 402 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 415 MET cc_start: 0.3648 (OUTLIER) cc_final: 0.3059 (mmm) REVERT: A 419 ASN cc_start: 0.7237 (m110) cc_final: 0.6848 (m110) REVERT: A 441 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4787 (pp-130) REVERT: A 461 GLU cc_start: 0.7587 (pm20) cc_final: 0.7059 (pm20) REVERT: A 494 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7248 (mtp-110) REVERT: A 514 ASP cc_start: 0.8505 (p0) cc_final: 0.7571 (t0) REVERT: A 581 ILE cc_start: 0.8355 (mm) cc_final: 0.8045 (mp) REVERT: A 726 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6818 (tpt-90) outliers start: 44 outliers final: 25 residues processed: 152 average time/residue: 0.4856 time to fit residues: 82.1323 Evaluate side-chains 149 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 157 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 GLN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.153467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112902 restraints weight = 17947.050| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.19 r_work: 0.3270 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12984 Z= 0.154 Angle : 0.591 9.169 17661 Z= 0.303 Chirality : 0.044 0.174 1926 Planarity : 0.005 0.061 2302 Dihedral : 4.328 23.845 1754 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.02 % Allowed : 14.83 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1598 helix: 0.39 (0.38), residues: 195 sheet: -0.08 (0.26), residues: 420 loop : -1.44 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.030 0.002 TYR B 676 PHE 0.026 0.002 PHE A 513 TRP 0.015 0.001 TRP A 722 HIS 0.008 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (12984) covalent geometry : angle 0.59098 / 0.30 (17661) hydrogen bonds : bond 0.04678 / 3.22 ( 360) hydrogen bonds : angle 5.07025 / 3.56 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 312 LEU cc_start: 0.8594 (mt) cc_final: 0.8317 (mt) REVERT: B 505 ASN cc_start: 0.7514 (p0) cc_final: 0.6502 (t0) REVERT: B 740 GLU cc_start: 0.6434 (tt0) cc_final: 0.5704 (pp20) REVERT: B 744 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6532 (tp30) REVERT: B 762 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6820 (tm-30) REVERT: B 817 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5697 (t80) REVERT: B 833 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7349 (pt0) REVERT: B 898 MET cc_start: 0.7853 (tpp) cc_final: 0.7644 (mmt) REVERT: A 158 LYS cc_start: 0.7744 (mppt) cc_final: 0.7358 (mppt) REVERT: A 252 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8502 (mm110) REVERT: A 383 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6324 (tp30) REVERT: A 391 PHE cc_start: 0.8319 (t80) cc_final: 0.8050 (t80) REVERT: A 402 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 415 MET cc_start: 0.3779 (OUTLIER) cc_final: 0.2416 (mmm) REVERT: A 419 ASN cc_start: 0.7247 (m110) cc_final: 0.7008 (m110) REVERT: A 441 MET cc_start: 0.5052 (OUTLIER) cc_final: 0.4793 (pp-130) REVERT: A 461 GLU cc_start: 0.7479 (pm20) cc_final: 0.6863 (pm20) REVERT: A 494 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7648 (mtp-110) REVERT: A 514 ASP cc_start: 0.8657 (p0) cc_final: 0.7768 (t0) REVERT: A 581 ILE cc_start: 0.8380 (mm) cc_final: 0.8081 (mp) REVERT: A 726 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6808 (tpt-90) outliers start: 42 outliers final: 24 residues processed: 151 average time/residue: 0.5212 time to fit residues: 87.2886 Evaluate side-chains 148 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 GLN ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.154752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114210 restraints weight = 18010.108| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.19 r_work: 0.3285 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12984 Z= 0.124 Angle : 0.567 9.059 17661 Z= 0.288 Chirality : 0.043 0.173 1926 Planarity : 0.005 0.060 2302 Dihedral : 4.181 24.676 1754 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 16.13 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1598 helix: 0.56 (0.38), residues: 195 sheet: -0.03 (0.26), residues: 420 loop : -1.39 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 144 TYR 0.024 0.001 TYR B 676 PHE 0.024 0.001 PHE A 513 TRP 0.016 0.001 TRP A 722 HIS 0.006 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (12984) covalent geometry : angle 0.56687 / 0.29 (17661) hydrogen bonds : bond 0.04216 / 2.90 ( 360) hydrogen bonds : angle 4.93812 / 3.47 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 312 LEU cc_start: 0.8595 (mt) cc_final: 0.8325 (mt) REVERT: B 505 ASN cc_start: 0.7489 (p0) cc_final: 0.6492 (t0) REVERT: B 740 GLU cc_start: 0.6440 (tt0) cc_final: 0.5718 (pp20) REVERT: B 762 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6843 (tm-30) REVERT: B 833 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7351 (pt0) REVERT: B 898 MET cc_start: 0.7831 (tpp) cc_final: 0.7631 (mmt) REVERT: A 158 LYS cc_start: 0.7736 (mppt) cc_final: 0.7395 (mppt) REVERT: A 252 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8526 (mm110) REVERT: A 383 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: A 391 PHE cc_start: 0.8297 (t80) cc_final: 0.8037 (t80) REVERT: A 402 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 415 MET cc_start: 0.3781 (OUTLIER) cc_final: 0.2195 (mmm) REVERT: A 419 ASN cc_start: 0.7290 (m110) cc_final: 0.7013 (m110) REVERT: A 441 MET cc_start: 0.5029 (OUTLIER) cc_final: 0.4788 (pp-130) REVERT: A 461 GLU cc_start: 0.7469 (pm20) cc_final: 0.6833 (pm20) REVERT: A 494 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7566 (mtp-110) REVERT: A 514 ASP cc_start: 0.8640 (p0) cc_final: 0.7758 (t0) REVERT: A 581 ILE cc_start: 0.8375 (mm) cc_final: 0.8085 (mp) REVERT: A 726 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6809 (tpt-90) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.4995 time to fit residues: 77.8484 Evaluate side-chains 138 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 chunk 17 optimal weight: 0.0010 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116947 restraints weight = 17822.707| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.21 r_work: 0.3326 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12984 Z= 0.095 Angle : 0.542 9.794 17661 Z= 0.272 Chirality : 0.042 0.176 1926 Planarity : 0.004 0.060 2302 Dihedral : 3.927 24.265 1754 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.87 % Allowed : 16.85 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1598 helix: 0.87 (0.39), residues: 190 sheet: 0.10 (0.26), residues: 420 loop : -1.29 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.030 0.001 TYR B 676 PHE 0.024 0.001 PHE A 513 TRP 0.018 0.001 TRP A 722 HIS 0.003 0.001 HIS B 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (12984) covalent geometry : angle 0.54171 / 0.27 (17661) hydrogen bonds : bond 0.03523 / 2.44 ( 360) hydrogen bonds : angle 4.73228 / 3.32 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 312 LEU cc_start: 0.8589 (mt) cc_final: 0.8319 (mt) REVERT: B 505 ASN cc_start: 0.7479 (p0) cc_final: 0.6454 (t0) REVERT: B 740 GLU cc_start: 0.6293 (tt0) cc_final: 0.5680 (pp20) REVERT: B 762 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6905 (tm-30) REVERT: B 833 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7343 (pt0) REVERT: B 898 MET cc_start: 0.7748 (tpp) cc_final: 0.7474 (mmt) REVERT: A 158 LYS cc_start: 0.7810 (mppt) cc_final: 0.7523 (mppt) REVERT: A 252 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8531 (mm110) REVERT: A 383 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6265 (tp30) REVERT: A 391 PHE cc_start: 0.8233 (t80) cc_final: 0.7679 (t80) REVERT: A 395 LEU cc_start: 0.7366 (tm) cc_final: 0.7061 (tm) REVERT: A 402 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 415 MET cc_start: 0.3605 (OUTLIER) cc_final: 0.2109 (mmm) REVERT: A 419 ASN cc_start: 0.7280 (m110) cc_final: 0.6977 (m110) REVERT: A 441 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4798 (pp-130) REVERT: A 461 GLU cc_start: 0.7467 (pm20) cc_final: 0.6817 (pm20) REVERT: A 486 TYR cc_start: 0.6332 (m-80) cc_final: 0.6047 (m-80) REVERT: A 494 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7583 (mtp-110) REVERT: A 514 ASP cc_start: 0.8605 (p0) cc_final: 0.7727 (t0) REVERT: A 726 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6818 (tpt-90) outliers start: 26 outliers final: 13 residues processed: 139 average time/residue: 0.5152 time to fit residues: 79.7115 Evaluate side-chains 134 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 149 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 0.0370 chunk 136 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116992 restraints weight = 17823.469| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.15 r_work: 0.3327 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12984 Z= 0.103 Angle : 0.548 9.737 17661 Z= 0.274 Chirality : 0.042 0.177 1926 Planarity : 0.004 0.062 2302 Dihedral : 3.892 24.302 1754 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.73 % Allowed : 17.21 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.21), residues: 1598 helix: 0.87 (0.38), residues: 196 sheet: 0.17 (0.26), residues: 418 loop : -1.27 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 144 TYR 0.027 0.001 TYR B 676 PHE 0.022 0.001 PHE A 513 TRP 0.018 0.001 TRP A 630 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (12984) covalent geometry : angle 0.54812 / 0.27 (17661) hydrogen bonds : bond 0.03655 / 2.53 ( 360) hydrogen bonds : angle 4.69125 / 3.30 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 505 ASN cc_start: 0.7492 (p0) cc_final: 0.6457 (t0) REVERT: B 740 GLU cc_start: 0.6301 (tt0) cc_final: 0.5688 (pp20) REVERT: B 762 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6898 (tm-30) REVERT: B 833 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7313 (pt0) REVERT: B 898 MET cc_start: 0.7757 (tpp) cc_final: 0.7470 (mmt) REVERT: A 158 LYS cc_start: 0.7771 (mppt) cc_final: 0.7456 (mppt) REVERT: A 252 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8532 (mm110) REVERT: A 383 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6328 (tp30) REVERT: A 391 PHE cc_start: 0.8223 (t80) cc_final: 0.7700 (t80) REVERT: A 402 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 419 ASN cc_start: 0.6982 (m110) cc_final: 0.6688 (m110) REVERT: A 461 GLU cc_start: 0.7441 (pm20) cc_final: 0.6758 (pm20) REVERT: A 486 TYR cc_start: 0.6435 (m-80) cc_final: 0.6178 (m-80) REVERT: A 494 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7562 (mtp-110) REVERT: A 514 ASP cc_start: 0.8617 (p0) cc_final: 0.7725 (t0) REVERT: A 726 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6832 (tpt-90) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 0.5194 time to fit residues: 80.0267 Evaluate side-chains 132 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 95 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 49 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116546 restraints weight = 18023.149| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.21 r_work: 0.3318 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12984 Z= 0.109 Angle : 0.569 9.593 17661 Z= 0.284 Chirality : 0.043 0.179 1926 Planarity : 0.004 0.062 2302 Dihedral : 3.911 24.419 1754 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.44 % Allowed : 17.78 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1598 helix: 0.91 (0.38), residues: 196 sheet: 0.20 (0.26), residues: 418 loop : -1.28 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 633 TYR 0.034 0.001 TYR B 676 PHE 0.021 0.001 PHE A 513 TRP 0.017 0.001 TRP A 630 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12984) covalent geometry : angle 0.56876 / 0.28 (17661) hydrogen bonds : bond 0.03701 / 2.56 ( 360) hydrogen bonds : angle 4.70393 / 3.30 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 505 ASN cc_start: 0.7506 (p0) cc_final: 0.6472 (t0) REVERT: B 740 GLU cc_start: 0.6300 (tt0) cc_final: 0.5727 (pp20) REVERT: B 762 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6910 (tm-30) REVERT: B 833 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7290 (pt0) REVERT: B 898 MET cc_start: 0.7772 (tpp) cc_final: 0.7479 (mmt) REVERT: A 158 LYS cc_start: 0.7787 (mppt) cc_final: 0.7422 (mppt) REVERT: A 252 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8536 (mm110) REVERT: A 383 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6264 (tp30) REVERT: A 391 PHE cc_start: 0.8198 (t80) cc_final: 0.7645 (t80) REVERT: A 402 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 415 MET cc_start: 0.4019 (mmm) cc_final: 0.2662 (mmt) REVERT: A 419 ASN cc_start: 0.7008 (m110) cc_final: 0.6678 (m110) REVERT: A 461 GLU cc_start: 0.7474 (pm20) cc_final: 0.6785 (pm20) REVERT: A 486 TYR cc_start: 0.6458 (m-80) cc_final: 0.6207 (m-80) REVERT: A 494 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7558 (mtp-110) REVERT: A 514 ASP cc_start: 0.8636 (p0) cc_final: 0.7736 (t0) outliers start: 20 outliers final: 17 residues processed: 131 average time/residue: 0.4890 time to fit residues: 71.3311 Evaluate side-chains 131 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ARG Chi-restraints excluded: chain A residue 766 ARG Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 7 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112806 restraints weight = 18140.627| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.19 r_work: 0.3274 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12984 Z= 0.169 Angle : 0.626 9.262 17661 Z= 0.317 Chirality : 0.044 0.177 1926 Planarity : 0.005 0.063 2302 Dihedral : 4.302 25.690 1754 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.66 % Allowed : 17.85 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1598 helix: 0.63 (0.37), residues: 199 sheet: 0.07 (0.26), residues: 422 loop : -1.43 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 633 TYR 0.036 0.002 TYR B 676 PHE 0.019 0.002 PHE A 513 TRP 0.015 0.001 TRP A 630 HIS 0.007 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (12984) covalent geometry : angle 0.62627 / 0.32 (17661) hydrogen bonds : bond 0.04783 / 3.29 ( 360) hydrogen bonds : angle 4.99002 / 3.50 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3424.42 seconds wall clock time: 59 minutes 18.80 seconds (3558.80 seconds total)