Starting phenix.real_space_refine on Sat Jul 4 02:03:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.map" model { file = "/net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ear_47841/07_2026/9ear_47841.cif" } resolution = 3.1 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= 0.002 sd= 0.033 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: 7 Type Number sf(0) Gaussians P 318 5.49 5 S 36 5.16 5 Be 1 3.05 5 C 10367 2.51 5 N 3313 2.21 5 O 3966 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18004 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 845 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3219 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "J" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3259 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "W" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5460 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 17, 'TRANS': 645} Chain breaks: 3 Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.80, per 1000 atoms: 0.21 Number of scatterers: 18004 At special positions: 0 Unit cell: (97.94, 151.06, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 318 15.00 F 3 9.00 O 3966 8.00 N 3313 7.00 C 10367 6.00 Be 1 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 506.0 milliseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 64.9% alpha, 5.8% beta 136 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.831A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.567A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.702A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.542A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.505A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.511A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.825A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.717A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.704A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.624A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.273A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.573A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 289 through 293 Processing helix chain 'W' and resid 296 through 301 Processing helix chain 'W' and resid 326 through 330 Processing helix chain 'W' and resid 334 through 342 removed outlier: 4.237A pdb=" N LEU W 338 " --> pdb=" O THR W 334 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS W 339 " --> pdb=" O GLU W 335 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 347 No H-bonds generated for 'chain 'W' and resid 345 through 347' Processing helix chain 'W' and resid 348 through 366 removed outlier: 3.996A pdb=" N TYR W 352 " --> pdb=" O LYS W 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN W 365 " --> pdb=" O ARG W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 367 through 388 removed outlier: 3.845A pdb=" N TYR W 388 " --> pdb=" O LEU W 384 " (cutoff:3.500A) Processing helix chain 'W' and resid 403 through 405 No H-bonds generated for 'chain 'W' and resid 403 through 405' Processing helix chain 'W' and resid 417 through 421 Processing helix chain 'W' and resid 425 through 446 removed outlier: 3.649A pdb=" N LYS W 432 " --> pdb=" O LEU W 428 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA W 435 " --> pdb=" O LYS W 431 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS W 436 " --> pdb=" O LYS W 432 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE W 437 " --> pdb=" O PHE W 433 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP W 438 " --> pdb=" O GLN W 434 " (cutoff:3.500A) Processing helix chain 'W' and resid 474 through 478 removed outlier: 3.715A pdb=" N GLU W 477 " --> pdb=" O GLY W 474 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 498 Processing helix chain 'W' and resid 511 through 526 removed outlier: 3.590A pdb=" N GLN W 515 " --> pdb=" O GLY W 511 " (cutoff:3.500A) Processing helix chain 'W' and resid 541 through 552 Processing helix chain 'W' and resid 564 through 575 Processing helix chain 'W' and resid 592 through 599 removed outlier: 3.557A pdb=" N LYS W 598 " --> pdb=" O GLU W 594 " (cutoff:3.500A) Processing helix chain 'W' and resid 599 through 604 removed outlier: 4.150A pdb=" N LEU W 603 " --> pdb=" O ASP W 599 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY W 604 " --> pdb=" O LYS W 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 599 through 604' Processing helix chain 'W' and resid 616 through 621 removed outlier: 4.181A pdb=" N ASN W 621 " --> pdb=" O ARG W 618 " (cutoff:3.500A) Processing helix chain 'W' and resid 624 through 632 removed outlier: 3.692A pdb=" N ASP W 632 " --> pdb=" O LYS W 628 " (cutoff:3.500A) Processing helix chain 'W' and resid 649 through 661 removed outlier: 3.751A pdb=" N LEU W 653 " --> pdb=" O SER W 649 " (cutoff:3.500A) Processing helix chain 'W' and resid 667 through 675 removed outlier: 3.796A pdb=" N PHE W 671 " --> pdb=" O SER W 667 " (cutoff:3.500A) Processing helix chain 'W' and resid 679 through 691 removed outlier: 4.084A pdb=" N TYR W 683 " --> pdb=" O ARG W 679 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA W 684 " --> pdb=" O GLU W 680 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU W 691 " --> pdb=" O HIS W 687 " (cutoff:3.500A) Processing helix chain 'W' and resid 698 through 703 removed outlier: 3.501A pdb=" N VAL W 702 " --> pdb=" O VAL W 698 " (cutoff:3.500A) Processing helix chain 'W' and resid 719 through 732 Processing helix chain 'W' and resid 733 through 738 removed outlier: 4.085A pdb=" N LEU W 737 " --> pdb=" O ASN W 733 " (cutoff:3.500A) Processing helix chain 'W' and resid 744 through 749 Processing helix chain 'W' and resid 750 through 761 Processing helix chain 'W' and resid 762 through 765 Processing helix chain 'W' and resid 775 through 787 removed outlier: 3.649A pdb=" N GLN W 781 " --> pdb=" O GLN W 777 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER W 787 " --> pdb=" O LEU W 783 " (cutoff:3.500A) Processing helix chain 'W' and resid 787 through 804 removed outlier: 3.695A pdb=" N ILE W 791 " --> pdb=" O SER W 787 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU W 792 " --> pdb=" O GLY W 788 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS W 795 " --> pdb=" O ILE W 791 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG W 803 " --> pdb=" O ARG W 799 " (cutoff:3.500A) Processing helix chain 'W' and resid 813 through 828 removed outlier: 3.783A pdb=" N TYR W 826 " --> pdb=" O GLU W 822 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG W 827 " --> pdb=" O TYR W 823 " (cutoff:3.500A) Processing helix chain 'W' and resid 839 through 852 removed outlier: 3.505A pdb=" N ARG W 843 " --> pdb=" O LYS W 839 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS W 844 " --> pdb=" O GLY W 840 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN W 845 " --> pdb=" O GLU W 841 " (cutoff:3.500A) Processing helix chain 'W' and resid 864 through 868 Processing helix chain 'W' and resid 887 through 896 removed outlier: 3.737A pdb=" N ASP W 891 " --> pdb=" O ASN W 887 " (cutoff:3.500A) Processing helix chain 'W' and resid 917 through 939 removed outlier: 3.804A pdb=" N ASP W 921 " --> pdb=" O SER W 917 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG W 925 " --> pdb=" O ASP W 921 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG W 939 " --> pdb=" O LEU W 935 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.856A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.685A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.727A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.832A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.056A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 391 through 402 removed outlier: 6.414A pdb=" N ILE W 394 " --> pdb=" O LYS W 412 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS W 412 " --> pdb=" O ILE W 394 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA W 396 " --> pdb=" O TYR W 410 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP W 408 " --> pdb=" O SER W 398 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN W 400 " --> pdb=" O TYR W 406 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR W 406 " --> pdb=" O GLN W 400 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER W 422 " --> pdb=" O CYS W 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 558 through 559 removed outlier: 4.028A pdb=" N LEU W 639 " --> pdb=" O ILE W 611 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU W 640 " --> pdb=" O CYS W 502 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE W 503 " --> pdb=" O LEU W 695 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 710 through 717 removed outlier: 6.103A pdb=" N VAL W 710 " --> pdb=" O ILE W 909 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG W 911 " --> pdb=" O VAL W 710 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN W 712 " --> pdb=" O ARG W 911 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL W 913 " --> pdb=" O GLN W 712 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU W 714 " --> pdb=" O VAL W 913 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS W 915 " --> pdb=" O LEU W 714 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N MET W 716 " --> pdb=" O LYS W 915 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL W 879 " --> pdb=" O TYR W 910 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU W 912 " --> pdb=" O VAL W 879 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE W 881 " --> pdb=" O LEU W 912 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR W 914 " --> pdb=" O ILE W 881 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU W 808 " --> pdb=" O VAL W 880 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN W 832 " --> pdb=" O LEU W 861 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N SER W 863 " --> pdb=" O GLN W 832 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU W 834 " --> pdb=" O SER W 863 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 4.99 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3366 1.33 - 1.45: 5789 1.45 - 1.57: 9146 1.57 - 1.69: 633 1.69 - 1.81: 59 Bond restraints: 18993 Sorted by residual: bond pdb=" CB ML3 A 4 " pdb=" SG ML3 A 4 " ideal model delta sigma weight residual 1.817 1.513 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" SG ML3 A 4 " pdb=" CD ML3 A 4 " ideal model delta sigma weight residual 1.815 1.520 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C1' DC J -40 " pdb=" N1 DC J -40 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.15e+01 bond pdb=" F2 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.567 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 18988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 26682 3.16 - 6.32: 281 6.32 - 9.47: 15 9.47 - 12.63: 11 12.63 - 15.79: 6 Bond angle restraints: 26995 Sorted by residual: angle pdb=" C3' DC J 60 " pdb=" O3' DC J 60 " pdb=" P DC J 61 " ideal model delta sigma weight residual 120.20 105.23 14.97 1.50e+00 4.44e-01 9.97e+01 angle pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " pdb=" P DA J 65 " ideal model delta sigma weight residual 120.20 105.64 14.56 1.50e+00 4.44e-01 9.42e+01 angle pdb=" C3' DG I -68 " pdb=" O3' DG I -68 " pdb=" P DA I -67 " ideal model delta sigma weight residual 120.20 105.91 14.29 1.50e+00 4.44e-01 9.08e+01 angle pdb=" C3' DA I -66 " pdb=" O3' DA I -66 " pdb=" P DT I -65 " ideal model delta sigma weight residual 120.20 106.51 13.69 1.50e+00 4.44e-01 8.33e+01 angle pdb=" C3' DA I -72 " pdb=" O3' DA I -72 " pdb=" P DT I -71 " ideal model delta sigma weight residual 120.20 107.68 12.52 1.50e+00 4.44e-01 6.97e+01 ... (remaining 26990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 9189 35.83 - 71.67: 1374 71.67 - 107.50: 16 107.50 - 143.33: 4 143.33 - 179.17: 10 Dihedral angle restraints: 10593 sinusoidal: 6454 harmonic: 4139 Sorted by residual: dihedral pdb=" O1B ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PB ADP W1501 " pdb=" PA ADP W1501 " ideal model delta sinusoidal sigma weight residual 300.00 120.83 179.17 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP W1501 " pdb=" O5' ADP W1501 " pdb=" PA ADP W1501 " pdb=" O2A ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 100.81 -160.81 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O2A ADP W1501 " pdb=" O3A ADP W1501 " pdb=" PA ADP W1501 " pdb=" PB ADP W1501 " ideal model delta sinusoidal sigma weight residual -60.00 52.89 -112.89 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 10590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 2837 0.138 - 0.277: 151 0.277 - 0.415: 3 0.415 - 0.553: 20 0.553 - 0.691: 3 Chirality restraints: 3014 Sorted by residual: chirality pdb=" P DA I -72 " pdb=" OP1 DA I -72 " pdb=" OP2 DA I -72 " pdb=" O5' DA I -72 " both_signs ideal model delta sigma weight residual True 2.34 -3.03 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" P DG J 73 " pdb=" OP1 DG J 73 " pdb=" OP2 DG J 73 " pdb=" O5' DG J 73 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P DC J 75 " pdb=" OP1 DC J 75 " pdb=" OP2 DC J 75 " pdb=" O5' DC J 75 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.81e+00 ... (remaining 3011 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 70 " -0.041 2.00e-02 2.50e+03 1.78e-02 9.54e+00 pdb=" N9 DG I 70 " 0.040 2.00e-02 2.50e+03 pdb=" C8 DG I 70 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 70 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 70 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 70 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 70 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG I 70 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG I 70 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG I 70 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DG I 70 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 70 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -60 " -0.031 2.00e-02 2.50e+03 1.70e-02 8.63e+00 pdb=" N9 DG I -60 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DG I -60 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG I -60 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I -60 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I -60 " -0.019 2.00e-02 2.50e+03 pdb=" O6 DG I -60 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG I -60 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG I -60 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -60 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -60 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I -60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.034 2.00e-02 2.50e+03 1.52e-02 6.39e+00 pdb=" N9 DA I -35 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.004 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 87 2.51 - 3.11: 12736 3.11 - 3.70: 29705 3.70 - 4.30: 43770 4.30 - 4.90: 65348 Nonbonded interactions: 151646 Sorted by model distance: nonbonded pdb=" O2B ADP W1501 " pdb="BE BEF W1502 " model vdw 1.909 2.420 nonbonded pdb=" OG SER W 719 " pdb=" OE1 GLN W 722 " model vdw 2.010 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.035 3.040 nonbonded pdb=" OG SER W 402 " pdb=" O TYR W 406 " model vdw 2.077 3.040 nonbonded pdb=" CZ ARG W 900 " pdb=" F1 BEF W1502 " model vdw 2.203 3.220 ... (remaining 151641 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.130 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.008 0.419 18996 Z= 0.635 Angle : 0.874 15.791 26995 Z= 0.680 Chirality : 0.072 0.691 3014 Planarity : 0.004 0.038 2320 Dihedral : 25.233 179.168 7921 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.25 % Allowed : 7.13 % Favored : 92.62 % 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: 1.62 (0.23), residues: 1395 helix: 1.95 (0.18), residues: 817 sheet: -0.18 (0.75), residues: 54 loop : -0.13 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 17 TYR 0.010 0.001 TYR W 410 PHE 0.009 0.001 PHE W 610 TRP 0.008 0.001 TRP W 552 HIS 0.004 0.001 HIS W 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.56 (18993) covalent geometry : angle 0.87448 / 0.68 (26995) hydrogen bonds : bond 0.12917 / 8.75 ( 975) hydrogen bonds : angle 5.06842 / 3.84 ( 2506) Misc. bond : bond 0.24507 / 11.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7056 (ttp80) REVERT: A 63 ARG cc_start: 0.7624 (mmp80) cc_final: 0.7099 (mmp80) REVERT: B 36 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.8075 (mtm180) REVERT: D 59 MET cc_start: 0.7684 (mmm) cc_final: 0.7466 (mmp) REVERT: E 53 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7673 (ttm170) REVERT: F 45 ARG cc_start: 0.8693 (ttt-90) cc_final: 0.8423 (ttt-90) REVERT: H 49 THR cc_start: 0.8741 (m) cc_final: 0.8450 (p) REVERT: H 56 MET cc_start: 0.8362 (tpp) cc_final: 0.7564 (tpp) REVERT: W 298 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6828 (pm20) REVERT: W 317 GLN cc_start: 0.5252 (mp10) cc_final: 0.4422 (mt0) REVERT: W 386 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7945 (mtmm) REVERT: W 433 PHE cc_start: 0.7683 (m-80) cc_final: 0.7351 (m-80) REVERT: W 434 GLN cc_start: 0.7389 (tp-100) cc_final: 0.6929 (tp-100) REVERT: W 437 ILE cc_start: 0.8466 (mp) cc_final: 0.7807 (tp) REVERT: W 485 GLN cc_start: 0.7908 (mt0) cc_final: 0.7619 (mt0) REVERT: W 503 ILE cc_start: 0.8299 (mt) cc_final: 0.8097 (mm) REVERT: W 516 THR cc_start: 0.8377 (m) cc_final: 0.8142 (m) REVERT: W 535 LEU cc_start: 0.8508 (mt) cc_final: 0.8203 (mp) REVERT: W 545 TRP cc_start: 0.8405 (m100) cc_final: 0.8092 (m100) REVERT: W 547 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7966 (mtt180) REVERT: W 600 LYS cc_start: 0.8319 (pttt) cc_final: 0.8069 (pttt) REVERT: W 610 PHE cc_start: 0.7101 (t80) cc_final: 0.6792 (t80) REVERT: W 613 VAL cc_start: 0.8171 (t) cc_final: 0.7836 (p) REVERT: W 627 TYR cc_start: 0.7614 (t80) cc_final: 0.7290 (t80) REVERT: W 628 LYS cc_start: 0.8127 (mttt) cc_final: 0.7846 (mtmm) REVERT: W 651 LYS cc_start: 0.7851 (tttm) cc_final: 0.7628 (tppp) REVERT: W 686 LEU cc_start: 0.7383 (mp) cc_final: 0.7122 (mp) REVERT: W 695 LEU cc_start: 0.8007 (tt) cc_final: 0.7595 (tp) REVERT: W 718 MET cc_start: 0.6310 (mtm) cc_final: 0.6110 (mtm) REVERT: W 723 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7146 (mttt) REVERT: W 729 ILE cc_start: 0.7914 (mt) cc_final: 0.7642 (tt) REVERT: W 795 LYS cc_start: 0.8123 (mttt) cc_final: 0.7790 (mmtp) REVERT: W 816 MET cc_start: 0.7933 (tpt) cc_final: 0.7710 (mmm) REVERT: W 822 GLU cc_start: 0.7400 (tp30) cc_final: 0.6829 (tp30) REVERT: W 828 GLN cc_start: 0.7749 (mt0) cc_final: 0.7346 (mt0) REVERT: W 832 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6502 (mm-40) REVERT: W 844 LYS cc_start: 0.7758 (tttm) cc_final: 0.7509 (tttm) REVERT: W 849 HIS cc_start: 0.7265 (t-90) cc_final: 0.6845 (t-90) REVERT: W 869 LEU cc_start: 0.6993 (mp) cc_final: 0.6729 (mp) REVERT: W 892 LEU cc_start: 0.8352 (tp) cc_final: 0.8050 (mm) REVERT: W 919 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6785 (mt-10) REVERT: W 921 ASP cc_start: 0.7089 (t0) cc_final: 0.6797 (t0) outliers start: 3 outliers final: 3 residues processed: 298 average time/residue: 0.1783 time to fit residues: 72.6062 Evaluate side-chains 271 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 268 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain W residue 625 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 HIS H 60 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 546 GLN W 648 ASN W 781 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112531 restraints weight = 27518.416| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.61 r_work: 0.3198 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 18996 Z= 0.342 Angle : 0.856 10.762 26995 Z= 0.474 Chirality : 0.060 0.465 3014 Planarity : 0.006 0.053 2320 Dihedral : 29.729 177.441 5049 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.21 % Allowed : 9.67 % Favored : 88.11 % 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: 1.05 (0.22), residues: 1395 helix: 1.56 (0.18), residues: 825 sheet: -0.32 (0.66), residues: 59 loop : -0.56 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 696 TYR 0.014 0.002 TYR E 41 PHE 0.023 0.002 PHE W 533 TRP 0.026 0.002 TRP W 491 HIS 0.011 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.34 (18993) covalent geometry : angle 0.85591 / 0.47 (26995) hydrogen bonds : bond 0.06630 / 4.56 ( 975) hydrogen bonds : angle 3.96737 / 2.98 ( 2506) Misc. bond : bond 0.01087 / 0.51 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7696 (ttp80) REVERT: B 36 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8356 (mtm180) REVERT: B 92 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8117 (mtp85) REVERT: C 77 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8238 (mtt180) REVERT: D 56 MET cc_start: 0.7970 (tpp) cc_final: 0.7604 (tpp) REVERT: D 59 MET cc_start: 0.7961 (mmm) cc_final: 0.7761 (mmp) REVERT: D 118 TYR cc_start: 0.8447 (t80) cc_final: 0.8148 (t80) REVERT: H 56 MET cc_start: 0.8352 (tpp) cc_final: 0.7842 (tpt) REVERT: W 317 GLN cc_start: 0.5155 (mp10) cc_final: 0.4459 (mt0) REVERT: W 339 LYS cc_start: 0.8323 (mttt) cc_final: 0.8080 (mttt) REVERT: W 412 LYS cc_start: 0.7955 (tptt) cc_final: 0.7499 (tptt) REVERT: W 416 LEU cc_start: 0.7870 (mt) cc_final: 0.7482 (mp) REVERT: W 433 PHE cc_start: 0.7988 (m-80) cc_final: 0.7759 (m-80) REVERT: W 434 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7116 (tp-100) REVERT: W 437 ILE cc_start: 0.8514 (mp) cc_final: 0.7934 (tp) REVERT: W 438 ASP cc_start: 0.7923 (m-30) cc_final: 0.7420 (m-30) REVERT: W 485 GLN cc_start: 0.8272 (mt0) cc_final: 0.7948 (mt0) REVERT: W 503 ILE cc_start: 0.8400 (mt) cc_final: 0.8149 (mm) REVERT: W 526 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7307 (mt-10) REVERT: W 535 LEU cc_start: 0.8487 (mt) cc_final: 0.8209 (mp) REVERT: W 600 LYS cc_start: 0.8506 (pttt) cc_final: 0.8254 (pttt) REVERT: W 620 LYS cc_start: 0.7836 (pttt) cc_final: 0.6439 (ttpt) REVERT: W 625 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8276 (mt) REVERT: W 651 LYS cc_start: 0.7896 (tttm) cc_final: 0.7679 (mttm) REVERT: W 661 MET cc_start: 0.7126 (mmm) cc_final: 0.6914 (mmm) REVERT: W 686 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7470 (mp) REVERT: W 700 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8176 (mtmm) REVERT: W 717 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7890 (mm-30) REVERT: W 729 ILE cc_start: 0.7913 (mt) cc_final: 0.7585 (tt) REVERT: W 734 TYR cc_start: 0.7597 (m-80) cc_final: 0.7254 (m-80) REVERT: W 735 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7424 (mmtp) REVERT: W 756 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7501 (mtpp) REVERT: W 757 LYS cc_start: 0.8070 (mttt) cc_final: 0.7402 (mmtp) REVERT: W 782 HIS cc_start: 0.7077 (t-90) cc_final: 0.6873 (t-170) REVERT: W 795 LYS cc_start: 0.8266 (mttt) cc_final: 0.8016 (mttt) REVERT: W 807 VAL cc_start: 0.7952 (t) cc_final: 0.7671 (p) REVERT: W 816 MET cc_start: 0.8124 (tpt) cc_final: 0.7780 (tmm) REVERT: W 822 GLU cc_start: 0.7771 (tp30) cc_final: 0.7176 (tp30) REVERT: W 839 LYS cc_start: 0.7610 (mttt) cc_final: 0.7293 (mmtt) REVERT: W 844 LYS cc_start: 0.7990 (tttm) cc_final: 0.7505 (tttm) REVERT: W 849 HIS cc_start: 0.7867 (t-90) cc_final: 0.7560 (t-170) REVERT: W 863 SER cc_start: 0.8220 (t) cc_final: 0.7978 (t) REVERT: W 892 LEU cc_start: 0.8413 (tp) cc_final: 0.8130 (mm) REVERT: W 919 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6828 (mt-10) REVERT: W 921 ASP cc_start: 0.7327 (t0) cc_final: 0.7038 (t0) outliers start: 27 outliers final: 14 residues processed: 315 average time/residue: 0.1849 time to fit residues: 80.4849 Evaluate side-chains 311 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 577 THR Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 686 LEU Chi-restraints excluded: chain W residue 722 GLN Chi-restraints excluded: chain W residue 913 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 24 GLN E 108 ASN ** W 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 387 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114924 restraints weight = 27682.361| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.56 r_work: 0.3238 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18996 Z= 0.168 Angle : 0.678 11.223 26995 Z= 0.390 Chirality : 0.049 0.410 3014 Planarity : 0.004 0.041 2320 Dihedral : 29.823 177.853 5046 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.80 % Allowed : 12.95 % Favored : 85.25 % 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: 1.53 (0.22), residues: 1395 helix: 1.99 (0.18), residues: 833 sheet: -0.21 (0.64), residues: 65 loop : -0.48 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 131 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.001 PHE W 463 TRP 0.048 0.003 TRP W 491 HIS 0.006 0.001 HIS W 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (18993) covalent geometry : angle 0.67777 / 0.39 (26995) hydrogen bonds : bond 0.05325 / 3.66 ( 975) hydrogen bonds : angle 3.61057 / 2.72 ( 2506) Misc. bond : bond 0.00071 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7729 (ttp80) REVERT: C 77 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8150 (mtt180) REVERT: C 81 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7731 (tpt170) REVERT: D 56 MET cc_start: 0.7956 (tpp) cc_final: 0.7606 (tpp) REVERT: D 118 TYR cc_start: 0.8455 (t80) cc_final: 0.7895 (t80) REVERT: E 72 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8244 (mtt90) REVERT: G 35 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7625 (ttt180) REVERT: G 97 LEU cc_start: 0.8490 (mp) cc_final: 0.8241 (mt) REVERT: W 284 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5806 (ttt180) REVERT: W 317 GLN cc_start: 0.5117 (mp10) cc_final: 0.4645 (mt0) REVERT: W 382 ASP cc_start: 0.7727 (p0) cc_final: 0.7314 (p0) REVERT: W 386 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7597 (mtmm) REVERT: W 412 LYS cc_start: 0.8005 (tptt) cc_final: 0.7538 (tptt) REVERT: W 416 LEU cc_start: 0.7940 (mt) cc_final: 0.7582 (mp) REVERT: W 437 ILE cc_start: 0.8477 (mp) cc_final: 0.7959 (tp) REVERT: W 485 GLN cc_start: 0.8162 (mt0) cc_final: 0.7882 (mt0) REVERT: W 496 TRP cc_start: 0.8410 (t60) cc_final: 0.8163 (t-100) REVERT: W 503 ILE cc_start: 0.8346 (mt) cc_final: 0.8134 (mm) REVERT: W 588 ILE cc_start: 0.8504 (mt) cc_final: 0.8250 (mt) REVERT: W 600 LYS cc_start: 0.8511 (pttt) cc_final: 0.8236 (pttt) REVERT: W 620 LYS cc_start: 0.7776 (pttt) cc_final: 0.6356 (ttpt) REVERT: W 628 LYS cc_start: 0.8512 (mttt) cc_final: 0.8138 (ttmm) REVERT: W 651 LYS cc_start: 0.7917 (tttm) cc_final: 0.7702 (mttm) REVERT: W 661 MET cc_start: 0.7054 (mmm) cc_final: 0.6819 (mmm) REVERT: W 697 ARG cc_start: 0.7598 (mpp80) cc_final: 0.7111 (mpp80) REVERT: W 699 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7273 (tptt) REVERT: W 700 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8120 (mtmm) REVERT: W 729 ILE cc_start: 0.7891 (mt) cc_final: 0.7594 (tt) REVERT: W 734 TYR cc_start: 0.7596 (m-80) cc_final: 0.7325 (m-80) REVERT: W 735 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7389 (mmtp) REVERT: W 756 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7486 (mtpp) REVERT: W 757 LYS cc_start: 0.7927 (mttt) cc_final: 0.7215 (mmmm) REVERT: W 782 HIS cc_start: 0.7225 (t-90) cc_final: 0.6928 (t-170) REVERT: W 795 LYS cc_start: 0.8271 (mttt) cc_final: 0.7991 (mttt) REVERT: W 807 VAL cc_start: 0.7946 (t) cc_final: 0.7659 (p) REVERT: W 816 MET cc_start: 0.8157 (tpt) cc_final: 0.7805 (tmm) REVERT: W 822 GLU cc_start: 0.7798 (tp30) cc_final: 0.6994 (tp30) REVERT: W 826 TYR cc_start: 0.6891 (m-10) cc_final: 0.6438 (m-10) REVERT: W 839 LYS cc_start: 0.7630 (mttt) cc_final: 0.7303 (mmtt) REVERT: W 844 LYS cc_start: 0.7938 (tttm) cc_final: 0.7587 (tttm) REVERT: W 849 HIS cc_start: 0.7893 (t-90) cc_final: 0.7579 (t-170) REVERT: W 863 SER cc_start: 0.8248 (t) cc_final: 0.8006 (t) REVERT: W 877 ASP cc_start: 0.7453 (m-30) cc_final: 0.7099 (m-30) REVERT: W 893 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7456 (tp-100) REVERT: W 903 GLN cc_start: 0.8432 (mm110) cc_final: 0.7673 (mm110) REVERT: W 919 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6788 (mt-10) REVERT: W 921 ASP cc_start: 0.7303 (t0) cc_final: 0.6977 (t0) REVERT: W 924 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7774 (mm-30) outliers start: 22 outliers final: 13 residues processed: 306 average time/residue: 0.1776 time to fit residues: 74.8652 Evaluate side-chains 310 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 293 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 483 ASP Chi-restraints excluded: chain W residue 543 THR Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 674 GLU Chi-restraints excluded: chain W residue 695 LEU Chi-restraints excluded: chain W residue 699 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 487 ASN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 828 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108397 restraints weight = 27595.381| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.62 r_work: 0.3127 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.105 18996 Z= 0.540 Angle : 0.948 10.850 26995 Z= 0.512 Chirality : 0.067 0.517 3014 Planarity : 0.007 0.068 2320 Dihedral : 30.003 175.828 5046 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.70 % Allowed : 14.75 % Favored : 82.54 % 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: 0.25 (0.22), residues: 1395 helix: 0.87 (0.17), residues: 827 sheet: -0.19 (0.68), residues: 66 loop : -0.88 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 696 TYR 0.023 0.003 TYR W 410 PHE 0.025 0.003 PHE F 100 TRP 0.061 0.003 TRP W 491 HIS 0.009 0.002 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.01135 / 0.54 (18993) covalent geometry : angle 0.94805 / 0.51 (26995) hydrogen bonds : bond 0.07684 / 5.35 ( 975) hydrogen bonds : angle 4.16710 / 3.11 ( 2506) Misc. bond : bond 0.00214 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7727 (ttp80) REVERT: C 77 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8203 (mtt180) REVERT: D 31 LYS cc_start: 0.8120 (pptt) cc_final: 0.7910 (pptt) REVERT: D 90 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: D 118 TYR cc_start: 0.8583 (t80) cc_final: 0.8358 (t80) REVERT: G 35 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7826 (ttt180) REVERT: H 31 LYS cc_start: 0.8224 (mttt) cc_final: 0.8006 (mttt) REVERT: W 278 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.3363 (ptp) REVERT: W 284 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5909 (ttt180) REVERT: W 317 GLN cc_start: 0.5061 (mp10) cc_final: 0.4810 (mt0) REVERT: W 346 MET cc_start: 0.6284 (mmm) cc_final: 0.5935 (mmt) REVERT: W 389 GLN cc_start: 0.8696 (mp10) cc_final: 0.8475 (mp10) REVERT: W 412 LYS cc_start: 0.7787 (tptt) cc_final: 0.7368 (tptt) REVERT: W 416 LEU cc_start: 0.8283 (mt) cc_final: 0.7870 (mp) REVERT: W 434 GLN cc_start: 0.8223 (tp40) cc_final: 0.8009 (tp40) REVERT: W 437 ILE cc_start: 0.8663 (mp) cc_final: 0.8134 (tp) REVERT: W 485 GLN cc_start: 0.8303 (mt0) cc_final: 0.7912 (mt0) REVERT: W 503 ILE cc_start: 0.8325 (mt) cc_final: 0.8056 (mm) REVERT: W 526 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7512 (mt-10) REVERT: W 588 ILE cc_start: 0.8501 (mt) cc_final: 0.8261 (mt) REVERT: W 599 ASP cc_start: 0.7618 (p0) cc_final: 0.7405 (p0) REVERT: W 600 LYS cc_start: 0.8630 (pttt) cc_final: 0.8380 (pttt) REVERT: W 613 VAL cc_start: 0.8541 (t) cc_final: 0.8205 (p) REVERT: W 620 LYS cc_start: 0.7992 (pttt) cc_final: 0.6722 (ttpt) REVERT: W 628 LYS cc_start: 0.8553 (mttt) cc_final: 0.8039 (ttmm) REVERT: W 651 LYS cc_start: 0.7936 (tttm) cc_final: 0.7697 (mttm) REVERT: W 661 MET cc_start: 0.7379 (mmm) cc_final: 0.7059 (mmm) REVERT: W 697 ARG cc_start: 0.7777 (mpp80) cc_final: 0.7212 (mpp80) REVERT: W 700 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8046 (ptpp) REVERT: W 729 ILE cc_start: 0.8016 (mt) cc_final: 0.7663 (tt) REVERT: W 735 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7465 (mmtp) REVERT: W 756 LYS cc_start: 0.8230 (mtpp) cc_final: 0.7613 (mtpp) REVERT: W 757 LYS cc_start: 0.8201 (mttt) cc_final: 0.7474 (mttm) REVERT: W 795 LYS cc_start: 0.8394 (mttt) cc_final: 0.8126 (mttt) REVERT: W 810 PHE cc_start: 0.7677 (m-80) cc_final: 0.7069 (m-80) REVERT: W 822 GLU cc_start: 0.7882 (tp30) cc_final: 0.7175 (tp30) REVERT: W 832 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7473 (mm-40) REVERT: W 839 LYS cc_start: 0.7650 (mttt) cc_final: 0.7316 (mmtt) REVERT: W 844 LYS cc_start: 0.8296 (tttm) cc_final: 0.8016 (tttm) REVERT: W 877 ASP cc_start: 0.7610 (m-30) cc_final: 0.7255 (m-30) REVERT: W 893 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7504 (tp-100) REVERT: W 903 GLN cc_start: 0.8603 (mm110) cc_final: 0.7863 (mm110) REVERT: W 919 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6909 (mt-10) REVERT: W 921 ASP cc_start: 0.7325 (t0) cc_final: 0.7002 (t0) REVERT: W 940 MET cc_start: 0.2008 (mpp) cc_final: 0.0542 (mtt) outliers start: 33 outliers final: 20 residues processed: 334 average time/residue: 0.1834 time to fit residues: 84.5777 Evaluate side-chains 338 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain W residue 278 MET Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 577 THR Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 694 LEU Chi-restraints excluded: chain W residue 764 LEU Chi-restraints excluded: chain W residue 778 GLU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN E 108 ASN ** W 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 469 GLN W 487 ASN W 546 GLN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 832 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113116 restraints weight = 27439.635| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.54 r_work: 0.3212 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18996 Z= 0.168 Angle : 0.687 14.276 26995 Z= 0.389 Chirality : 0.050 0.396 3014 Planarity : 0.005 0.045 2320 Dihedral : 30.076 179.186 5046 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.62 % Allowed : 15.57 % Favored : 81.80 % 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 (0.22), residues: 1395 helix: 1.71 (0.18), residues: 827 sheet: 0.04 (0.67), residues: 65 loop : -0.59 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.015 0.002 TYR F 98 PHE 0.031 0.002 PHE W 671 TRP 0.037 0.002 TRP W 491 HIS 0.009 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (18993) covalent geometry : angle 0.68674 / 0.39 (26995) hydrogen bonds : bond 0.05323 / 3.61 ( 975) hydrogen bonds : angle 3.60136 / 2.70 ( 2506) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7695 (ttp80) REVERT: B 92 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8126 (mtp85) REVERT: C 77 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8141 (mtt180) REVERT: C 96 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (tp) REVERT: D 31 LYS cc_start: 0.8129 (pptt) cc_final: 0.7883 (pptt) REVERT: D 56 MET cc_start: 0.7952 (tpp) cc_final: 0.7633 (tpp) REVERT: D 90 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: E 72 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8334 (mtt90) REVERT: G 35 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7726 (ttt180) REVERT: W 278 MET cc_start: 0.5082 (OUTLIER) cc_final: 0.4734 (mpp) REVERT: W 284 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5947 (ttt180) REVERT: W 285 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7582 (mmpt) REVERT: W 302 ASP cc_start: 0.6520 (t0) cc_final: 0.4312 (m-30) REVERT: W 317 GLN cc_start: 0.4900 (mp10) cc_final: 0.4544 (mt0) REVERT: W 386 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7771 (mmtm) REVERT: W 389 GLN cc_start: 0.8746 (mp10) cc_final: 0.8369 (mp10) REVERT: W 416 LEU cc_start: 0.8178 (mt) cc_final: 0.7971 (mp) REVERT: W 437 ILE cc_start: 0.8504 (mp) cc_final: 0.8019 (tp) REVERT: W 485 GLN cc_start: 0.8199 (mt0) cc_final: 0.7893 (mt0) REVERT: W 503 ILE cc_start: 0.8324 (mt) cc_final: 0.8074 (mm) REVERT: W 536 VAL cc_start: 0.8590 (t) cc_final: 0.8225 (m) REVERT: W 560 VAL cc_start: 0.8845 (m) cc_final: 0.8550 (p) REVERT: W 588 ILE cc_start: 0.8459 (mt) cc_final: 0.8207 (mt) REVERT: W 600 LYS cc_start: 0.8582 (pttt) cc_final: 0.8323 (pttt) REVERT: W 613 VAL cc_start: 0.8530 (t) cc_final: 0.8280 (m) REVERT: W 628 LYS cc_start: 0.8535 (mttt) cc_final: 0.8192 (mtpp) REVERT: W 661 MET cc_start: 0.7148 (mmm) cc_final: 0.6834 (mmm) REVERT: W 718 MET cc_start: 0.6736 (ttm) cc_final: 0.6311 (ttm) REVERT: W 723 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7443 (mtmm) REVERT: W 729 ILE cc_start: 0.7956 (mt) cc_final: 0.7641 (tt) REVERT: W 735 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7420 (mmtp) REVERT: W 768 PRO cc_start: 0.7209 (Cg_endo) cc_final: 0.6972 (Cg_exo) REVERT: W 782 HIS cc_start: 0.7274 (t-90) cc_final: 0.6822 (t-170) REVERT: W 795 LYS cc_start: 0.8340 (mttt) cc_final: 0.8018 (mmtp) REVERT: W 810 PHE cc_start: 0.7615 (m-80) cc_final: 0.7060 (m-80) REVERT: W 812 GLN cc_start: 0.7155 (pt0) cc_final: 0.6933 (pt0) REVERT: W 822 GLU cc_start: 0.7874 (tp30) cc_final: 0.7133 (tp30) REVERT: W 826 TYR cc_start: 0.7030 (m-10) cc_final: 0.6463 (m-10) REVERT: W 832 GLN cc_start: 0.7631 (mm110) cc_final: 0.7276 (mm110) REVERT: W 839 LYS cc_start: 0.7682 (mttt) cc_final: 0.7350 (mmtt) REVERT: W 869 LEU cc_start: 0.7147 (mp) cc_final: 0.6753 (tt) REVERT: W 877 ASP cc_start: 0.7484 (m-30) cc_final: 0.6332 (m-30) REVERT: W 879 VAL cc_start: 0.8162 (t) cc_final: 0.7718 (m) REVERT: W 893 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7772 (tp-100) REVERT: W 895 GLN cc_start: 0.8108 (mt0) cc_final: 0.7853 (tt0) REVERT: W 903 GLN cc_start: 0.8454 (mm110) cc_final: 0.7822 (mm110) REVERT: W 919 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6853 (mt-10) REVERT: W 921 ASP cc_start: 0.7244 (t0) cc_final: 0.6874 (t0) outliers start: 32 outliers final: 16 residues processed: 317 average time/residue: 0.1737 time to fit residues: 77.0345 Evaluate side-chains 328 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain W residue 278 MET Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 577 THR Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 778 GLU Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 0.0670 chunk 128 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN E 108 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 469 GLN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 828 GLN W 899 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113655 restraints weight = 27242.319| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.53 r_work: 0.3217 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18996 Z= 0.168 Angle : 0.667 13.268 26995 Z= 0.377 Chirality : 0.049 0.405 3014 Planarity : 0.005 0.047 2320 Dihedral : 30.049 178.952 5044 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.54 % Allowed : 16.39 % 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: 1.44 (0.23), residues: 1395 helix: 1.94 (0.18), residues: 827 sheet: 0.10 (0.64), residues: 66 loop : -0.58 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 40 TYR 0.013 0.001 TYR F 51 PHE 0.012 0.001 PHE A 67 TRP 0.067 0.002 TRP W 491 HIS 0.009 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (18993) covalent geometry : angle 0.66717 / 0.38 (26995) hydrogen bonds : bond 0.05031 / 3.44 ( 975) hydrogen bonds : angle 3.55447 / 2.66 ( 2506) Misc. bond : bond 0.00054 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 303 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7740 (ttp80) REVERT: B 92 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8127 (mtp85) REVERT: C 77 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8198 (mtt180) REVERT: D 31 LYS cc_start: 0.8166 (pptt) cc_final: 0.7874 (pptt) REVERT: D 56 MET cc_start: 0.7923 (tpp) cc_final: 0.7577 (tpp) REVERT: D 90 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: E 72 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8333 (mtt90) REVERT: H 103 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7716 (mp) REVERT: W 284 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.6024 (ttt180) REVERT: W 298 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7362 (pm20) REVERT: W 302 ASP cc_start: 0.6474 (t0) cc_final: 0.4271 (m-30) REVERT: W 386 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7788 (mmtm) REVERT: W 389 GLN cc_start: 0.8753 (mp10) cc_final: 0.8479 (mp10) REVERT: W 393 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7161 (ttt180) REVERT: W 416 LEU cc_start: 0.8173 (mt) cc_final: 0.7957 (mp) REVERT: W 437 ILE cc_start: 0.8477 (mp) cc_final: 0.7968 (tp) REVERT: W 485 GLN cc_start: 0.8231 (mt0) cc_final: 0.7927 (mt0) REVERT: W 503 ILE cc_start: 0.8295 (mt) cc_final: 0.8030 (mm) REVERT: W 526 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7199 (mt-10) REVERT: W 536 VAL cc_start: 0.8557 (t) cc_final: 0.8195 (m) REVERT: W 560 VAL cc_start: 0.8850 (m) cc_final: 0.8553 (p) REVERT: W 575 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6734 (mt-10) REVERT: W 588 ILE cc_start: 0.8452 (mt) cc_final: 0.8176 (mt) REVERT: W 600 LYS cc_start: 0.8604 (pttt) cc_final: 0.8335 (pttt) REVERT: W 613 VAL cc_start: 0.8530 (t) cc_final: 0.8269 (m) REVERT: W 628 LYS cc_start: 0.8518 (mttt) cc_final: 0.8231 (mtpp) REVERT: W 661 MET cc_start: 0.7121 (mmm) cc_final: 0.6627 (mmm) REVERT: W 718 MET cc_start: 0.6672 (ttm) cc_final: 0.6224 (ttm) REVERT: W 723 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7401 (mtmm) REVERT: W 727 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7834 (ptmm) REVERT: W 729 ILE cc_start: 0.7929 (mt) cc_final: 0.7633 (tt) REVERT: W 735 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7416 (mmtp) REVERT: W 768 PRO cc_start: 0.7178 (Cg_endo) cc_final: 0.6963 (Cg_exo) REVERT: W 782 HIS cc_start: 0.7321 (t-90) cc_final: 0.6865 (t-170) REVERT: W 795 LYS cc_start: 0.8366 (mttt) cc_final: 0.7907 (mmtp) REVERT: W 810 PHE cc_start: 0.7612 (m-80) cc_final: 0.7096 (m-80) REVERT: W 812 GLN cc_start: 0.7039 (pt0) cc_final: 0.6812 (pt0) REVERT: W 822 GLU cc_start: 0.7866 (tp30) cc_final: 0.7125 (tp30) REVERT: W 828 GLN cc_start: 0.8240 (mm110) cc_final: 0.8001 (mp10) REVERT: W 839 LYS cc_start: 0.7635 (mttt) cc_final: 0.7299 (mmtt) REVERT: W 869 LEU cc_start: 0.7203 (mp) cc_final: 0.6784 (tt) REVERT: W 877 ASP cc_start: 0.7512 (m-30) cc_final: 0.7230 (m-30) REVERT: W 893 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7689 (tp-100) REVERT: W 895 GLN cc_start: 0.8097 (mt0) cc_final: 0.7857 (tt0) REVERT: W 903 GLN cc_start: 0.8469 (mm110) cc_final: 0.7818 (mm110) REVERT: W 919 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6855 (mt-10) REVERT: W 921 ASP cc_start: 0.7238 (t0) cc_final: 0.6862 (t0) outliers start: 31 outliers final: 21 residues processed: 316 average time/residue: 0.1767 time to fit residues: 78.2418 Evaluate side-chains 326 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 577 THR Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 751 ILE Chi-restraints excluded: chain W residue 764 LEU Chi-restraints excluded: chain W residue 778 GLU Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 141 optimal weight: 0.0020 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 113 optimal weight: 0.0970 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 469 GLN W 527 HIS W 675 HIS ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 899 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114895 restraints weight = 27562.406| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.56 r_work: 0.3244 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18996 Z= 0.137 Angle : 0.630 13.070 26995 Z= 0.359 Chirality : 0.046 0.401 3014 Planarity : 0.004 0.042 2320 Dihedral : 29.996 179.791 5044 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.13 % Allowed : 17.38 % 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: 1.61 (0.23), residues: 1395 helix: 2.04 (0.18), residues: 835 sheet: 0.39 (0.64), residues: 65 loop : -0.53 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 40 TYR 0.011 0.001 TYR D 80 PHE 0.013 0.001 PHE A 67 TRP 0.050 0.002 TRP W 491 HIS 0.011 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (18993) covalent geometry : angle 0.63049 / 0.36 (26995) hydrogen bonds : bond 0.04729 / 3.22 ( 975) hydrogen bonds : angle 3.41048 / 2.55 ( 2506) Misc. bond : bond 0.00043 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7730 (ttp80) REVERT: B 92 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8082 (mtp85) REVERT: C 65 LEU cc_start: 0.8585 (mt) cc_final: 0.8218 (mp) REVERT: C 77 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8191 (mtt180) REVERT: D 31 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7805 (pptt) REVERT: D 56 MET cc_start: 0.7889 (tpp) cc_final: 0.7671 (tpp) REVERT: D 90 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: E 72 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8311 (mtt90) REVERT: W 284 ARG cc_start: 0.6320 (OUTLIER) cc_final: 0.6000 (ttt180) REVERT: W 302 ASP cc_start: 0.6448 (t0) cc_final: 0.4376 (m-30) REVERT: W 318 TYR cc_start: 0.6563 (t80) cc_final: 0.6176 (t80) REVERT: W 352 TYR cc_start: 0.7685 (t80) cc_final: 0.7436 (t80) REVERT: W 389 GLN cc_start: 0.8756 (mp10) cc_final: 0.8542 (mp10) REVERT: W 393 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7064 (ttt180) REVERT: W 416 LEU cc_start: 0.8097 (mt) cc_final: 0.7873 (mp) REVERT: W 437 ILE cc_start: 0.8456 (mp) cc_final: 0.8012 (tp) REVERT: W 485 GLN cc_start: 0.8200 (mt0) cc_final: 0.7932 (mt0) REVERT: W 498 LYS cc_start: 0.7635 (mttt) cc_final: 0.7166 (mttp) REVERT: W 503 ILE cc_start: 0.8263 (mt) cc_final: 0.7976 (mm) REVERT: W 526 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7101 (mt-10) REVERT: W 536 VAL cc_start: 0.8564 (t) cc_final: 0.8204 (m) REVERT: W 560 VAL cc_start: 0.8837 (m) cc_final: 0.8538 (p) REVERT: W 575 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6883 (mt-10) REVERT: W 588 ILE cc_start: 0.8437 (mt) cc_final: 0.8214 (mt) REVERT: W 600 LYS cc_start: 0.8606 (pttt) cc_final: 0.8348 (pttt) REVERT: W 613 VAL cc_start: 0.8554 (t) cc_final: 0.8281 (m) REVERT: W 628 LYS cc_start: 0.8522 (mttt) cc_final: 0.8225 (mtpp) REVERT: W 661 MET cc_start: 0.7145 (mmm) cc_final: 0.6737 (mmm) REVERT: W 672 GLU cc_start: 0.7948 (tt0) cc_final: 0.7740 (tt0) REVERT: W 697 ARG cc_start: 0.7295 (mpp80) cc_final: 0.6978 (mpp80) REVERT: W 718 MET cc_start: 0.6599 (ttm) cc_final: 0.6097 (ttm) REVERT: W 723 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7270 (mtmm) REVERT: W 727 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7780 (ptmm) REVERT: W 729 ILE cc_start: 0.7897 (mt) cc_final: 0.7609 (tt) REVERT: W 735 LYS cc_start: 0.7868 (mmtp) cc_final: 0.7431 (mmtp) REVERT: W 768 PRO cc_start: 0.7157 (Cg_endo) cc_final: 0.6934 (Cg_exo) REVERT: W 795 LYS cc_start: 0.8338 (mttt) cc_final: 0.8003 (mmtp) REVERT: W 810 PHE cc_start: 0.7592 (m-80) cc_final: 0.7081 (m-80) REVERT: W 812 GLN cc_start: 0.7028 (pt0) cc_final: 0.6799 (pt0) REVERT: W 822 GLU cc_start: 0.7864 (tp30) cc_final: 0.7176 (tp30) REVERT: W 869 LEU cc_start: 0.7210 (mp) cc_final: 0.6864 (tt) REVERT: W 877 ASP cc_start: 0.7528 (m-30) cc_final: 0.7265 (m-30) REVERT: W 903 GLN cc_start: 0.8443 (mm110) cc_final: 0.7743 (tp-100) REVERT: W 919 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6869 (mt-10) REVERT: W 921 ASP cc_start: 0.7220 (t0) cc_final: 0.6822 (t0) REVERT: W 940 MET cc_start: 0.1675 (mpp) cc_final: 0.1375 (mpp) outliers start: 26 outliers final: 15 residues processed: 318 average time/residue: 0.1668 time to fit residues: 74.5622 Evaluate side-chains 320 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 751 ILE Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 157 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 138 optimal weight: 0.0060 chunk 121 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 899 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114138 restraints weight = 27406.170| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.55 r_work: 0.3228 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18996 Z= 0.174 Angle : 0.649 13.088 26995 Z= 0.366 Chirality : 0.048 0.430 3014 Planarity : 0.004 0.044 2320 Dihedral : 29.973 179.561 5044 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.21 % Allowed : 18.20 % Favored : 79.59 % 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: 1.60 (0.23), residues: 1395 helix: 2.02 (0.18), residues: 836 sheet: 0.33 (0.63), residues: 65 loop : -0.50 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 40 TYR 0.012 0.001 TYR F 51 PHE 0.011 0.001 PHE D 67 TRP 0.058 0.002 TRP W 491 HIS 0.015 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (18993) covalent geometry : angle 0.64947 / 0.37 (26995) hydrogen bonds : bond 0.04902 / 3.36 ( 975) hydrogen bonds : angle 3.44491 / 2.57 ( 2506) Misc. bond : bond 0.00079 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7705 (ttp80) REVERT: B 92 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8140 (mtp85) REVERT: C 77 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8234 (mtt180) REVERT: D 31 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7726 (pptt) REVERT: D 56 MET cc_start: 0.7949 (tpp) cc_final: 0.7646 (tpp) REVERT: D 90 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: H 103 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7706 (mp) REVERT: W 284 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.6054 (ttt180) REVERT: W 302 ASP cc_start: 0.6397 (t0) cc_final: 0.4203 (m-30) REVERT: W 346 MET cc_start: 0.6066 (mmm) cc_final: 0.5536 (mmm) REVERT: W 352 TYR cc_start: 0.7702 (t80) cc_final: 0.7454 (t80) REVERT: W 386 LYS cc_start: 0.8450 (mppt) cc_final: 0.8016 (mmtm) REVERT: W 393 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.7145 (ttt180) REVERT: W 416 LEU cc_start: 0.8118 (mt) cc_final: 0.7895 (mp) REVERT: W 437 ILE cc_start: 0.8507 (mp) cc_final: 0.8053 (tp) REVERT: W 485 GLN cc_start: 0.8189 (mt0) cc_final: 0.7932 (mt0) REVERT: W 498 LYS cc_start: 0.7674 (mttt) cc_final: 0.7345 (mmmm) REVERT: W 503 ILE cc_start: 0.8223 (mt) cc_final: 0.7986 (mm) REVERT: W 507 GLU cc_start: 0.7927 (tt0) cc_final: 0.7601 (tt0) REVERT: W 526 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7214 (mt-10) REVERT: W 536 VAL cc_start: 0.8570 (t) cc_final: 0.8217 (m) REVERT: W 560 VAL cc_start: 0.8845 (m) cc_final: 0.8540 (p) REVERT: W 575 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6875 (mt-10) REVERT: W 588 ILE cc_start: 0.8436 (mt) cc_final: 0.8158 (mt) REVERT: W 600 LYS cc_start: 0.8610 (pttt) cc_final: 0.8352 (pttt) REVERT: W 613 VAL cc_start: 0.8563 (t) cc_final: 0.8288 (m) REVERT: W 628 LYS cc_start: 0.8536 (mttt) cc_final: 0.8231 (mtpp) REVERT: W 661 MET cc_start: 0.7203 (mmm) cc_final: 0.6823 (mmm) REVERT: W 697 ARG cc_start: 0.7287 (mpp80) cc_final: 0.6933 (mpp80) REVERT: W 718 MET cc_start: 0.6610 (ttm) cc_final: 0.6139 (ttm) REVERT: W 723 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7338 (mtmm) REVERT: W 727 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7855 (ptmm) REVERT: W 729 ILE cc_start: 0.7916 (mt) cc_final: 0.7624 (tt) REVERT: W 735 LYS cc_start: 0.7867 (mmtp) cc_final: 0.7427 (mmtp) REVERT: W 768 PRO cc_start: 0.7170 (Cg_endo) cc_final: 0.6960 (Cg_exo) REVERT: W 795 LYS cc_start: 0.8374 (mttt) cc_final: 0.8036 (mmtp) REVERT: W 812 GLN cc_start: 0.7051 (pt0) cc_final: 0.6846 (pt0) REVERT: W 822 GLU cc_start: 0.7873 (tp30) cc_final: 0.7167 (tp30) REVERT: W 839 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7341 (mmtt) REVERT: W 869 LEU cc_start: 0.7278 (mp) cc_final: 0.6893 (tt) REVERT: W 877 ASP cc_start: 0.7507 (m-30) cc_final: 0.7229 (m-30) REVERT: W 893 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7696 (tp-100) REVERT: W 895 GLN cc_start: 0.8106 (mt0) cc_final: 0.7764 (tt0) REVERT: W 903 GLN cc_start: 0.8463 (mm110) cc_final: 0.7825 (mm110) REVERT: W 919 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6875 (mt-10) REVERT: W 921 ASP cc_start: 0.7222 (t0) cc_final: 0.6812 (t0) outliers start: 27 outliers final: 20 residues processed: 316 average time/residue: 0.1813 time to fit residues: 80.4808 Evaluate side-chains 323 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 508 MET Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 577 THR Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 751 ILE Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 121 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 389 GLN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 899 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114399 restraints weight = 27323.855| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.56 r_work: 0.3232 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18996 Z= 0.160 Angle : 0.634 10.881 26995 Z= 0.360 Chirality : 0.047 0.417 3014 Planarity : 0.004 0.052 2320 Dihedral : 29.936 179.269 5044 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.54 % Allowed : 17.95 % Favored : 79.51 % 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: 1.64 (0.23), residues: 1395 helix: 2.04 (0.18), residues: 836 sheet: 0.45 (0.62), residues: 65 loop : -0.46 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 40 TYR 0.013 0.001 TYR D 80 PHE 0.031 0.001 PHE W 671 TRP 0.057 0.002 TRP W 491 HIS 0.017 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (18993) covalent geometry : angle 0.63365 / 0.36 (26995) hydrogen bonds : bond 0.04832 / 3.30 ( 975) hydrogen bonds : angle 3.41093 / 2.55 ( 2506) Misc. bond : bond 0.00060 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7715 (ttp80) REVERT: B 92 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (mtp85) REVERT: C 65 LEU cc_start: 0.8582 (mt) cc_final: 0.8355 (mp) REVERT: C 77 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8224 (mtt180) REVERT: C 96 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8197 (tp) REVERT: D 31 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7732 (pptt) REVERT: D 56 MET cc_start: 0.7952 (tpp) cc_final: 0.7669 (tpp) REVERT: D 90 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: H 103 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7700 (mp) REVERT: W 284 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.6035 (ttt180) REVERT: W 302 ASP cc_start: 0.6377 (t0) cc_final: 0.4184 (m-30) REVERT: W 346 MET cc_start: 0.6041 (mmm) cc_final: 0.5517 (mmm) REVERT: W 352 TYR cc_start: 0.7693 (t80) cc_final: 0.7449 (t80) REVERT: W 386 LYS cc_start: 0.8400 (mppt) cc_final: 0.7827 (mmtm) REVERT: W 393 ARG cc_start: 0.7687 (mtp-110) cc_final: 0.7100 (ttt180) REVERT: W 416 LEU cc_start: 0.8147 (mt) cc_final: 0.7941 (mp) REVERT: W 437 ILE cc_start: 0.8502 (mp) cc_final: 0.8061 (tp) REVERT: W 485 GLN cc_start: 0.8160 (mt0) cc_final: 0.7930 (mt0) REVERT: W 492 LEU cc_start: 0.8481 (mt) cc_final: 0.8212 (mm) REVERT: W 498 LYS cc_start: 0.7677 (mttt) cc_final: 0.7320 (mmmm) REVERT: W 503 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7979 (mm) REVERT: W 507 GLU cc_start: 0.7956 (tt0) cc_final: 0.7752 (tt0) REVERT: W 526 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7169 (mt-10) REVERT: W 536 VAL cc_start: 0.8570 (t) cc_final: 0.8228 (m) REVERT: W 560 VAL cc_start: 0.8858 (m) cc_final: 0.8544 (p) REVERT: W 575 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6819 (mt-10) REVERT: W 588 ILE cc_start: 0.8423 (mt) cc_final: 0.8165 (mt) REVERT: W 600 LYS cc_start: 0.8601 (pttt) cc_final: 0.8346 (pttt) REVERT: W 613 VAL cc_start: 0.8546 (t) cc_final: 0.8276 (m) REVERT: W 628 LYS cc_start: 0.8552 (mttt) cc_final: 0.8246 (mtpp) REVERT: W 661 MET cc_start: 0.7198 (mmm) cc_final: 0.6822 (mmm) REVERT: W 668 TRP cc_start: 0.7992 (t-100) cc_final: 0.7537 (t-100) REVERT: W 672 GLU cc_start: 0.8093 (tt0) cc_final: 0.7773 (tt0) REVERT: W 703 GLU cc_start: 0.6391 (tm-30) cc_final: 0.6142 (tm-30) REVERT: W 718 MET cc_start: 0.6617 (ttm) cc_final: 0.6153 (ttm) REVERT: W 723 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7344 (mtmm) REVERT: W 727 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7860 (ptmm) REVERT: W 729 ILE cc_start: 0.7921 (mt) cc_final: 0.7629 (tt) REVERT: W 735 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7431 (mmtp) REVERT: W 795 LYS cc_start: 0.8365 (mttt) cc_final: 0.7902 (mmtp) REVERT: W 812 GLN cc_start: 0.7032 (pt0) cc_final: 0.6826 (pt0) REVERT: W 822 GLU cc_start: 0.7853 (tp30) cc_final: 0.7155 (tp30) REVERT: W 839 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7325 (mmtt) REVERT: W 877 ASP cc_start: 0.7499 (m-30) cc_final: 0.6637 (m-30) REVERT: W 903 GLN cc_start: 0.8453 (mm110) cc_final: 0.7637 (tp40) REVERT: W 905 LYS cc_start: 0.6583 (ttpt) cc_final: 0.6342 (tttt) REVERT: W 919 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6841 (mt-10) REVERT: W 921 ASP cc_start: 0.7225 (t0) cc_final: 0.6822 (t0) outliers start: 31 outliers final: 20 residues processed: 312 average time/residue: 0.1811 time to fit residues: 78.6230 Evaluate side-chains 320 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 389 GLN Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 489 LEU Chi-restraints excluded: chain W residue 503 ILE Chi-restraints excluded: chain W residue 508 MET Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 895 GLN W 899 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115200 restraints weight = 27171.994| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.54 r_work: 0.3243 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18996 Z= 0.144 Angle : 0.627 11.176 26995 Z= 0.356 Chirality : 0.046 0.406 3014 Planarity : 0.004 0.058 2320 Dihedral : 29.918 179.538 5044 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.30 % Allowed : 18.77 % Favored : 78.93 % 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: 1.68 (0.23), residues: 1395 helix: 2.08 (0.18), residues: 836 sheet: 0.46 (0.62), residues: 65 loop : -0.46 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 40 TYR 0.020 0.001 TYR W 388 PHE 0.028 0.001 PHE W 671 TRP 0.074 0.002 TRP W 491 HIS 0.026 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (18993) covalent geometry : angle 0.62730 / 0.36 (26995) hydrogen bonds : bond 0.04755 / 3.25 ( 975) hydrogen bonds : angle 3.39467 / 2.54 ( 2506) Misc. bond : bond 0.00056 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7687 (ttp80) REVERT: B 92 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8092 (mtp85) REVERT: C 65 LEU cc_start: 0.8593 (mt) cc_final: 0.8366 (mp) REVERT: C 77 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8220 (mtt180) REVERT: C 96 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8205 (tp) REVERT: D 31 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7731 (pptt) REVERT: D 56 MET cc_start: 0.7943 (tpp) cc_final: 0.7687 (tpp) REVERT: D 90 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: H 103 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7687 (mp) REVERT: W 284 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.6158 (ttt180) REVERT: W 298 GLU cc_start: 0.7759 (mp0) cc_final: 0.7491 (mp0) REVERT: W 302 ASP cc_start: 0.6382 (t0) cc_final: 0.4184 (m-30) REVERT: W 346 MET cc_start: 0.5982 (mmm) cc_final: 0.5463 (mmm) REVERT: W 352 TYR cc_start: 0.7654 (t80) cc_final: 0.7405 (t80) REVERT: W 386 LYS cc_start: 0.8169 (mppt) cc_final: 0.7635 (mmtm) REVERT: W 393 ARG cc_start: 0.7680 (mtp-110) cc_final: 0.7113 (ttt180) REVERT: W 416 LEU cc_start: 0.8150 (mt) cc_final: 0.7925 (mp) REVERT: W 437 ILE cc_start: 0.8474 (mp) cc_final: 0.8027 (tp) REVERT: W 485 GLN cc_start: 0.8091 (mt0) cc_final: 0.7865 (mt0) REVERT: W 492 LEU cc_start: 0.8427 (mt) cc_final: 0.8199 (mm) REVERT: W 498 LYS cc_start: 0.7658 (mttt) cc_final: 0.7304 (mmmm) REVERT: W 503 ILE cc_start: 0.8204 (mt) cc_final: 0.7968 (mm) REVERT: W 507 GLU cc_start: 0.7963 (tt0) cc_final: 0.7749 (tt0) REVERT: W 526 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7139 (mt-10) REVERT: W 536 VAL cc_start: 0.8567 (t) cc_final: 0.8218 (m) REVERT: W 560 VAL cc_start: 0.8857 (m) cc_final: 0.8545 (p) REVERT: W 575 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6456 (mt-10) REVERT: W 588 ILE cc_start: 0.8442 (mt) cc_final: 0.8162 (mt) REVERT: W 600 LYS cc_start: 0.8601 (pttt) cc_final: 0.8346 (pttt) REVERT: W 613 VAL cc_start: 0.8542 (t) cc_final: 0.8280 (m) REVERT: W 628 LYS cc_start: 0.8542 (mttt) cc_final: 0.8241 (mtpp) REVERT: W 661 MET cc_start: 0.7195 (mmm) cc_final: 0.6813 (mmm) REVERT: W 668 TRP cc_start: 0.8006 (t-100) cc_final: 0.7347 (t-100) REVERT: W 718 MET cc_start: 0.6590 (ttm) cc_final: 0.6110 (ttm) REVERT: W 723 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7319 (mtmm) REVERT: W 727 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7861 (ptmm) REVERT: W 729 ILE cc_start: 0.7947 (mt) cc_final: 0.7649 (tt) REVERT: W 735 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7452 (mmtp) REVERT: W 795 LYS cc_start: 0.8360 (mttt) cc_final: 0.7894 (mmtp) REVERT: W 812 GLN cc_start: 0.7037 (pt0) cc_final: 0.6828 (pt0) REVERT: W 822 GLU cc_start: 0.7826 (tp30) cc_final: 0.7125 (tp30) REVERT: W 839 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7307 (mmtt) REVERT: W 877 ASP cc_start: 0.7506 (m-30) cc_final: 0.7251 (m-30) REVERT: W 903 GLN cc_start: 0.8456 (mm110) cc_final: 0.7738 (tp-100) REVERT: W 909 ILE cc_start: 0.7954 (mt) cc_final: 0.7573 (mp) REVERT: W 919 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6862 (mt-10) REVERT: W 921 ASP cc_start: 0.7190 (t0) cc_final: 0.6767 (t0) outliers start: 28 outliers final: 19 residues processed: 309 average time/residue: 0.1719 time to fit residues: 74.4854 Evaluate side-chains 321 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain W residue 284 ARG Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 489 LEU Chi-restraints excluded: chain W residue 508 MET Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 892 LEU Chi-restraints excluded: chain W residue 895 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 134 optimal weight: 0.0980 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 144 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 487 ASN ** W 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 895 GLN W 899 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.150696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115485 restraints weight = 27391.414| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.54 r_work: 0.3223 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18996 Z= 0.143 Angle : 0.780 59.198 26995 Z= 0.451 Chirality : 0.046 0.405 3014 Planarity : 0.004 0.041 2320 Dihedral : 29.920 179.548 5044 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.46 % Allowed : 18.52 % Favored : 79.02 % 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: 1.69 (0.23), residues: 1395 helix: 2.08 (0.18), residues: 836 sheet: 0.47 (0.62), residues: 65 loop : -0.44 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 443 TYR 0.016 0.001 TYR W 388 PHE 0.027 0.001 PHE W 671 TRP 0.071 0.003 TRP W 491 HIS 0.022 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (18993) covalent geometry : angle 0.77986 / 0.45 (26995) hydrogen bonds : bond 0.04746 / 3.24 ( 975) hydrogen bonds : angle 3.40019 / 2.54 ( 2506) Misc. bond : bond 0.00056 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.64 seconds wall clock time: 91 minutes 20.38 seconds (5480.38 seconds total)