Starting phenix.real_space_refine on Sun May 18 22:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ear_47841/05_2025/9ear_47841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ear_47841/05_2025/9ear_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_47841/05_2025/9ear_47841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ear_47841/05_2025/9ear_47841.map" model { file = "/net/cci-nas-00/data/ceres_data/9ear_47841/05_2025/9ear_47841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ear_47841/05_2025/9ear_47841.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.69, per 1000 atoms: 0.54 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: 4.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 8.45 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: 10.85 Time building geometry restraints manager: 5.17 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=" 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 bond pdb=" F1 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.555 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" F3 BEF W1502 " pdb="BE BEF W1502 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 18988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 26817 3.16 - 6.32: 146 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 - 0.136: 2985 0.136 - 0.272: 3 0.272 - 0.409: 3 0.409 - 0.545: 20 0.545 - 0.681: 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 2.35 -3.03 -0.68 2.00e-01 2.50e+01 1.16e+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 2.35 -3.01 -0.66 2.00e-01 2.50e+01 1.10e+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 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.52e+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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 48.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.419 18996 Z= 0.409 Angle : 0.791 15.791 26995 Z= 0.462 Chirality : 0.060 0.681 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP W 552 HIS 0.004 0.001 HIS W 574 PHE 0.009 0.001 PHE W 610 TYR 0.010 0.001 TYR W 410 ARG 0.004 0.001 ARG C 17 Details of bonding type rmsd hydrogen bonds : bond 0.12917 ( 975) hydrogen bonds : angle 5.06842 ( 2506) covalent geometry : bond 0.00568 (18993) covalent geometry : angle 0.79101 (26995) Misc. bond : bond 0.24507 ( 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 : 1.350 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: 0.7467 (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: 0.7565 (tpp) REVERT: W 298 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6828 (pm20) REVERT: W 317 GLN cc_start: 0.5253 (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: 0.4214 time to fit residues: 168.7987 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 : 1.345 ------------------------------------------------------------------------------- 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 141 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS H 60 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 546 GLN W 648 ASN ** W 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115014 restraints weight = 27632.193| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.56 r_work: 0.3224 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18996 Z= 0.232 Angle : 0.640 9.577 26995 Z= 0.372 Chirality : 0.041 0.199 3014 Planarity : 0.004 0.039 2320 Dihedral : 29.598 175.002 5049 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.80 % Allowed : 9.75 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1395 helix: 2.18 (0.18), residues: 828 sheet: -0.06 (0.72), residues: 54 loop : -0.26 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 496 HIS 0.006 0.001 HIS G 31 PHE 0.024 0.002 PHE W 533 TYR 0.011 0.001 TYR W 484 ARG 0.005 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 975) hydrogen bonds : angle 3.53215 ( 2506) covalent geometry : bond 0.00523 (18993) covalent geometry : angle 0.63980 (26995) Misc. bond : bond 0.00127 ( 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 330 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 1.362 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: 0.7691 (ttp80) REVERT: A 63 ARG cc_start: 0.7463 (mmp80) cc_final: 0.6914 (mmp80) REVERT: C 77 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8230 (mtt90) REVERT: D 31 LYS cc_start: 0.8098 (pptt) cc_final: 0.7768 (pptt) REVERT: D 43 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8124 (mmmm) REVERT: D 59 MET cc_start: 0.7925 (mmm) cc_final: 0.7697 (mmp) REVERT: D 118 TYR cc_start: 0.8472 (t80) cc_final: 0.7966 (t80) REVERT: E 63 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8173 (mmp80) REVERT: H 56 MET cc_start: 0.8327 (tpp) cc_final: 0.8021 (tmm) REVERT: W 317 GLN cc_start: 0.5264 (mp10) cc_final: 0.4933 (mt0) REVERT: W 339 LYS cc_start: 0.8500 (mttt) cc_final: 0.8192 (mttt) REVERT: W 412 LYS cc_start: 0.7982 (tptt) cc_final: 0.7512 (tptt) REVERT: W 416 LEU cc_start: 0.7937 (mt) cc_final: 0.7613 (mp) REVERT: W 434 GLN cc_start: 0.7644 (tp-100) cc_final: 0.7322 (tp40) REVERT: W 437 ILE cc_start: 0.8422 (mp) cc_final: 0.7884 (tp) REVERT: W 485 GLN cc_start: 0.8211 (mt0) cc_final: 0.7867 (mt0) REVERT: W 503 ILE cc_start: 0.8365 (mt) cc_final: 0.8107 (mm) REVERT: W 510 LEU cc_start: 0.8537 (mt) cc_final: 0.8336 (mt) REVERT: W 535 LEU cc_start: 0.8507 (mt) cc_final: 0.8197 (mp) REVERT: W 588 ILE cc_start: 0.8508 (mt) cc_final: 0.8290 (mt) REVERT: W 600 LYS cc_start: 0.8523 (pttt) cc_final: 0.8246 (pttt) REVERT: W 613 VAL cc_start: 0.8357 (t) cc_final: 0.8004 (p) REVERT: W 661 MET cc_start: 0.7006 (mmm) cc_final: 0.6785 (mmm) REVERT: W 686 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7462 (mp) REVERT: W 697 ARG cc_start: 0.7619 (mpp80) cc_final: 0.6951 (mpp80) REVERT: W 700 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8069 (mtmm) REVERT: W 718 MET cc_start: 0.6454 (mtm) cc_final: 0.6223 (mtm) REVERT: W 722 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: W 724 GLN cc_start: 0.7867 (tt0) cc_final: 0.7626 (tp40) REVERT: W 729 ILE cc_start: 0.7894 (mt) cc_final: 0.7588 (tt) REVERT: W 734 TYR cc_start: 0.7602 (m-80) cc_final: 0.7354 (m-80) REVERT: W 735 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7385 (mmtp) REVERT: W 756 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7486 (mtpp) REVERT: W 757 LYS cc_start: 0.7880 (mttt) cc_final: 0.7158 (mmmm) REVERT: W 782 HIS cc_start: 0.7103 (t-90) cc_final: 0.6872 (t-170) REVERT: W 795 LYS cc_start: 0.8327 (mttt) cc_final: 0.8108 (mttt) REVERT: W 810 PHE cc_start: 0.7665 (m-80) cc_final: 0.7384 (m-80) REVERT: W 816 MET cc_start: 0.8174 (tpt) cc_final: 0.7772 (tmm) REVERT: W 822 GLU cc_start: 0.7812 (tp30) cc_final: 0.7039 (tp30) REVERT: W 826 TYR cc_start: 0.6825 (m-10) cc_final: 0.6376 (m-10) REVERT: W 832 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7071 (mm-40) REVERT: W 839 LYS cc_start: 0.7588 (mttt) cc_final: 0.7251 (mmtt) REVERT: W 849 HIS cc_start: 0.7903 (t-90) cc_final: 0.7593 (t-170) REVERT: W 863 SER cc_start: 0.8187 (t) cc_final: 0.7956 (t) REVERT: W 869 LEU cc_start: 0.7152 (mp) cc_final: 0.6741 (tt) REVERT: W 877 ASP cc_start: 0.7369 (m-30) cc_final: 0.7054 (m-30) REVERT: W 892 LEU cc_start: 0.8366 (tp) cc_final: 0.8076 (mm) REVERT: W 893 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7738 (tp-100) REVERT: W 903 GLN cc_start: 0.8413 (mm110) cc_final: 0.7216 (mm110) REVERT: W 919 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6769 (mt-10) REVERT: W 921 ASP cc_start: 0.7294 (t0) cc_final: 0.6959 (t0) outliers start: 22 outliers final: 13 residues processed: 316 average time/residue: 0.4240 time to fit residues: 182.0372 Evaluate side-chains 323 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 307 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 E residue 58 THR 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 483 ASP Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 565 ILE 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 778 GLU Chi-restraints excluded: chain W residue 814 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 61 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 93 GLN E 108 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 781 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 = 0.3869 r_free = 0.3869 target = 0.149887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115016 restraints weight = 27378.314| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.53 r_work: 0.3232 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18996 Z= 0.199 Angle : 0.593 8.417 26995 Z= 0.346 Chirality : 0.038 0.213 3014 Planarity : 0.004 0.039 2320 Dihedral : 29.414 174.541 5044 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.97 % Allowed : 12.46 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.23), residues: 1395 helix: 2.26 (0.18), residues: 828 sheet: -0.11 (0.62), residues: 65 loop : -0.22 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP W 491 HIS 0.005 0.001 HIS W 385 PHE 0.017 0.002 PHE W 671 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 975) hydrogen bonds : angle 3.37200 ( 2506) covalent geometry : bond 0.00447 (18993) covalent geometry : angle 0.59283 (26995) Misc. bond : bond 0.00080 ( 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 336 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7663 (ttp80) REVERT: A 72 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.8307 (mtt-85) REVERT: B 92 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7922 (mtp85) REVERT: C 77 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8206 (mtt180) REVERT: C 81 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7913 (tpt170) REVERT: D 31 LYS cc_start: 0.8156 (pptt) cc_final: 0.7790 (pptt) REVERT: D 43 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8082 (mmmm) REVERT: D 56 MET cc_start: 0.8077 (tpp) cc_final: 0.7748 (tmm) REVERT: D 59 MET cc_start: 0.7917 (mmm) cc_final: 0.7703 (mmp) REVERT: D 118 TYR cc_start: 0.8550 (t80) cc_final: 0.8218 (t80) REVERT: F 85 ASP cc_start: 0.7812 (m-30) cc_final: 0.7538 (m-30) REVERT: H 56 MET cc_start: 0.8347 (tpp) cc_final: 0.8063 (tmm) REVERT: W 317 GLN cc_start: 0.5418 (mp10) cc_final: 0.4797 (mt0) REVERT: W 339 LYS cc_start: 0.8503 (mttt) cc_final: 0.8282 (mttt) REVERT: W 385 HIS cc_start: 0.7894 (m170) cc_final: 0.7597 (m170) REVERT: W 386 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8119 (mtmt) REVERT: W 388 TYR cc_start: 0.8233 (m-10) cc_final: 0.8032 (m-10) REVERT: W 389 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7601 (mm-40) REVERT: W 416 LEU cc_start: 0.8093 (mt) cc_final: 0.7786 (mp) REVERT: W 433 PHE cc_start: 0.7955 (m-80) cc_final: 0.7727 (m-80) REVERT: W 434 GLN cc_start: 0.7479 (tp-100) cc_final: 0.6803 (tp-100) REVERT: W 437 ILE cc_start: 0.8424 (mp) cc_final: 0.7918 (tp) REVERT: W 485 GLN cc_start: 0.8272 (mt0) cc_final: 0.7916 (mt0) REVERT: W 496 TRP cc_start: 0.8445 (t60) cc_final: 0.8195 (t-100) REVERT: W 503 ILE cc_start: 0.8298 (mt) cc_final: 0.8046 (mm) REVERT: W 507 GLU cc_start: 0.8023 (tt0) cc_final: 0.7582 (tt0) REVERT: W 535 LEU cc_start: 0.8539 (mt) cc_final: 0.8218 (mp) REVERT: W 588 ILE cc_start: 0.8499 (mt) cc_final: 0.8288 (mt) REVERT: W 600 LYS cc_start: 0.8552 (pttt) cc_final: 0.8300 (pttt) REVERT: W 613 VAL cc_start: 0.8421 (t) cc_final: 0.8078 (m) REVERT: W 628 LYS cc_start: 0.8480 (mttt) cc_final: 0.8001 (ttmm) REVERT: W 651 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7457 (mttm) REVERT: W 661 MET cc_start: 0.7079 (mmm) cc_final: 0.6778 (mmm) REVERT: W 699 LYS cc_start: 0.8155 (mttt) cc_final: 0.7860 (mtmt) REVERT: W 700 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8140 (mtmm) REVERT: W 710 VAL cc_start: 0.7822 (t) cc_final: 0.7491 (t) REVERT: W 729 ILE cc_start: 0.7898 (mt) cc_final: 0.7586 (tt) REVERT: W 735 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7404 (mmtp) REVERT: W 756 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7469 (mtpp) REVERT: W 757 LYS cc_start: 0.7839 (mttt) cc_final: 0.7057 (mmtp) REVERT: W 768 PRO cc_start: 0.7206 (Cg_endo) cc_final: 0.6977 (Cg_exo) REVERT: W 795 LYS cc_start: 0.8359 (mttt) cc_final: 0.8117 (mttt) REVERT: W 810 PHE cc_start: 0.7600 (m-80) cc_final: 0.7264 (m-80) REVERT: W 816 MET cc_start: 0.8132 (tpt) cc_final: 0.7885 (tmm) REVERT: W 822 GLU cc_start: 0.7845 (tp30) cc_final: 0.7185 (tp30) REVERT: W 826 TYR cc_start: 0.7008 (m-10) cc_final: 0.6481 (m-10) REVERT: W 849 HIS cc_start: 0.7993 (t-90) cc_final: 0.7722 (t-170) REVERT: W 863 SER cc_start: 0.8192 (t) cc_final: 0.7948 (t) REVERT: W 869 LEU cc_start: 0.7114 (mp) cc_final: 0.6705 (tt) REVERT: W 877 ASP cc_start: 0.7379 (m-30) cc_final: 0.7101 (m-30) REVERT: W 893 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7778 (tp-100) REVERT: W 919 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6805 (mt-10) REVERT: W 921 ASP cc_start: 0.7233 (t0) cc_final: 0.6832 (t0) outliers start: 24 outliers final: 15 residues processed: 321 average time/residue: 0.3988 time to fit residues: 174.8217 Evaluate side-chains 326 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 307 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 81 ARG Chi-restraints excluded: chain C residue 101 THR 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 108 LEU Chi-restraints excluded: chain G residue 116 LEU 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 651 LYS Chi-restraints excluded: chain W residue 674 GLU Chi-restraints excluded: chain W residue 812 GLN Chi-restraints excluded: chain W residue 824 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN W 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115226 restraints weight = 27352.480| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.55 r_work: 0.3233 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18996 Z= 0.192 Angle : 0.582 9.504 26995 Z= 0.338 Chirality : 0.038 0.206 3014 Planarity : 0.004 0.039 2320 Dihedral : 29.326 173.410 5044 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.97 % Allowed : 13.44 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.22), residues: 1395 helix: 2.23 (0.18), residues: 836 sheet: -0.05 (0.61), residues: 65 loop : -0.31 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP W 491 HIS 0.003 0.001 HIS B 75 PHE 0.025 0.001 PHE W 671 TYR 0.011 0.001 TYR W 484 ARG 0.005 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 975) hydrogen bonds : angle 3.30501 ( 2506) covalent geometry : bond 0.00432 (18993) covalent geometry : angle 0.58168 (26995) Misc. bond : bond 0.00064 ( 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 328 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7711 (ttp80) REVERT: B 78 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: B 92 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: C 77 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: D 31 LYS cc_start: 0.8204 (pptt) cc_final: 0.7829 (pptt) REVERT: D 56 MET cc_start: 0.8006 (tpp) cc_final: 0.7779 (tmm) REVERT: D 118 TYR cc_start: 0.8561 (t80) cc_final: 0.8354 (t80) REVERT: H 56 MET cc_start: 0.8344 (tpp) cc_final: 0.8055 (tmm) REVERT: W 318 TYR cc_start: 0.6571 (t80) cc_final: 0.6088 (t80) REVERT: W 339 LYS cc_start: 0.8473 (mttt) cc_final: 0.8259 (mttt) REVERT: W 352 TYR cc_start: 0.7638 (t80) cc_final: 0.7412 (t80) REVERT: W 385 HIS cc_start: 0.7940 (m170) cc_final: 0.7553 (m170) REVERT: W 386 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8129 (mtmt) REVERT: W 387 GLN cc_start: 0.8079 (mt0) cc_final: 0.7564 (mt0) REVERT: W 389 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7782 (mm-40) REVERT: W 416 LEU cc_start: 0.8158 (mt) cc_final: 0.7924 (mp) REVERT: W 437 ILE cc_start: 0.8440 (mp) cc_final: 0.7982 (tp) REVERT: W 485 GLN cc_start: 0.8220 (mt0) cc_final: 0.7893 (mt0) REVERT: W 498 LYS cc_start: 0.7701 (mttt) cc_final: 0.7466 (mttt) REVERT: W 503 ILE cc_start: 0.8225 (mt) cc_final: 0.8006 (mm) REVERT: W 507 GLU cc_start: 0.8050 (tt0) cc_final: 0.7782 (tt0) REVERT: W 588 ILE cc_start: 0.8465 (mt) cc_final: 0.8236 (mt) REVERT: W 600 LYS cc_start: 0.8564 (pttt) cc_final: 0.8313 (pttt) REVERT: W 613 VAL cc_start: 0.8478 (t) cc_final: 0.8169 (m) REVERT: W 628 LYS cc_start: 0.8485 (mttt) cc_final: 0.8155 (ttmm) REVERT: W 661 MET cc_start: 0.7189 (mmm) cc_final: 0.6834 (mmm) REVERT: W 699 LYS cc_start: 0.8313 (mttt) cc_final: 0.8106 (mtmt) REVERT: W 700 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8197 (mtmm) REVERT: W 729 ILE cc_start: 0.7915 (mt) cc_final: 0.7625 (tt) REVERT: W 735 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7446 (mmtp) REVERT: W 756 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7464 (mtpp) REVERT: W 757 LYS cc_start: 0.7800 (mttt) cc_final: 0.7195 (mmmm) REVERT: W 795 LYS cc_start: 0.8398 (mttt) cc_final: 0.8153 (mttt) REVERT: W 810 PHE cc_start: 0.7601 (m-80) cc_final: 0.7245 (m-80) REVERT: W 822 GLU cc_start: 0.7849 (tp30) cc_final: 0.7129 (tp30) REVERT: W 826 TYR cc_start: 0.7135 (m-10) cc_final: 0.6548 (m-10) REVERT: W 839 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7336 (mmmt) REVERT: W 849 HIS cc_start: 0.8035 (t-90) cc_final: 0.7758 (t-170) REVERT: W 869 LEU cc_start: 0.7194 (mp) cc_final: 0.6914 (tt) REVERT: W 877 ASP cc_start: 0.7410 (m-30) cc_final: 0.7148 (m-30) REVERT: W 893 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7860 (tp-100) REVERT: W 919 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6840 (mt-10) REVERT: W 921 ASP cc_start: 0.7226 (t0) cc_final: 0.6814 (t0) outliers start: 24 outliers final: 16 residues processed: 310 average time/residue: 0.3982 time to fit residues: 169.6325 Evaluate side-chains 320 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 302 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 530 TYR 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 584 LEU Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 651 LYS Chi-restraints excluded: chain W residue 674 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 546 GLN ** W 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110524 restraints weight = 27426.712| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.58 r_work: 0.3163 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 18996 Z= 0.380 Angle : 0.693 10.362 26995 Z= 0.397 Chirality : 0.048 0.179 3014 Planarity : 0.005 0.052 2320 Dihedral : 29.576 173.136 5044 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.62 % Allowed : 14.02 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1395 helix: 1.67 (0.18), residues: 838 sheet: -0.14 (0.61), residues: 66 loop : -0.58 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP W 491 HIS 0.005 0.001 HIS D 46 PHE 0.032 0.002 PHE W 463 TYR 0.017 0.002 TYR W 410 ARG 0.007 0.001 ARG W 697 Details of bonding type rmsd hydrogen bonds : bond 0.05658 ( 975) hydrogen bonds : angle 3.63849 ( 2506) covalent geometry : bond 0.00863 (18993) covalent geometry : angle 0.69280 (26995) Misc. bond : bond 0.00115 ( 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 358 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7703 (ttp80) REVERT: A 72 ARG cc_start: 0.8580 (mtt-85) cc_final: 0.8320 (mtt-85) REVERT: B 92 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: C 77 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8095 (mtt180) REVERT: D 31 LYS cc_start: 0.8220 (pptt) cc_final: 0.7869 (pptt) REVERT: D 90 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: F 85 ASP cc_start: 0.7902 (m-30) cc_final: 0.7667 (m-30) REVERT: H 56 MET cc_start: 0.8393 (tpp) cc_final: 0.7628 (tpp) REVERT: H 110 GLU cc_start: 0.8210 (mm-30) cc_final: 0.8002 (mm-30) REVERT: W 302 ASP cc_start: 0.6695 (t0) cc_final: 0.4356 (m-30) REVERT: W 318 TYR cc_start: 0.6917 (t80) cc_final: 0.6219 (t80) REVERT: W 335 GLU cc_start: 0.6681 (tp30) cc_final: 0.6403 (tp30) REVERT: W 339 LYS cc_start: 0.8526 (mttt) cc_final: 0.8251 (mttt) REVERT: W 387 GLN cc_start: 0.8238 (mt0) cc_final: 0.7843 (mt0) REVERT: W 412 LYS cc_start: 0.7727 (tptp) cc_final: 0.7279 (tptt) REVERT: W 416 LEU cc_start: 0.8176 (mt) cc_final: 0.7740 (mp) REVERT: W 485 GLN cc_start: 0.8275 (mt0) cc_final: 0.7881 (mt0) REVERT: W 491 TRP cc_start: 0.7907 (t60) cc_final: 0.7651 (t60) REVERT: W 498 LYS cc_start: 0.7811 (mttt) cc_final: 0.7600 (mttt) REVERT: W 507 GLU cc_start: 0.7940 (tt0) cc_final: 0.7721 (tt0) REVERT: W 526 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7255 (mt-10) REVERT: W 588 ILE cc_start: 0.8486 (mt) cc_final: 0.8261 (mt) REVERT: W 599 ASP cc_start: 0.7594 (p0) cc_final: 0.7380 (p0) REVERT: W 600 LYS cc_start: 0.8612 (pttt) cc_final: 0.8383 (pttt) REVERT: W 613 VAL cc_start: 0.8566 (t) cc_final: 0.8232 (m) REVERT: W 625 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8014 (mt) REVERT: W 628 LYS cc_start: 0.8565 (mttt) cc_final: 0.8238 (ttmm) REVERT: W 661 MET cc_start: 0.7406 (mmm) cc_final: 0.7039 (mmm) REVERT: W 691 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7097 (tm-30) REVERT: W 700 LYS cc_start: 0.8743 (mtmm) cc_final: 0.7984 (ptpp) REVERT: W 712 GLN cc_start: 0.7675 (pm20) cc_final: 0.7466 (pm20) REVERT: W 717 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7865 (mm-30) REVERT: W 719 SER cc_start: 0.7151 (t) cc_final: 0.6833 (p) REVERT: W 729 ILE cc_start: 0.7983 (mt) cc_final: 0.7586 (tt) REVERT: W 735 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7478 (mmtp) REVERT: W 756 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7500 (mtpp) REVERT: W 757 LYS cc_start: 0.7999 (mttt) cc_final: 0.7268 (mmmm) REVERT: W 795 LYS cc_start: 0.8409 (mttt) cc_final: 0.8142 (mttt) REVERT: W 810 PHE cc_start: 0.7617 (m-80) cc_final: 0.7216 (m-80) REVERT: W 822 GLU cc_start: 0.7914 (tp30) cc_final: 0.7295 (tp30) REVERT: W 824 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7770 (mp) REVERT: W 832 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7404 (mm-40) REVERT: W 839 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7362 (mmtt) REVERT: W 877 ASP cc_start: 0.7475 (m-30) cc_final: 0.7170 (m-30) REVERT: W 909 ILE cc_start: 0.8138 (mp) cc_final: 0.7915 (mt) REVERT: W 919 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6932 (mt-10) REVERT: W 921 ASP cc_start: 0.7256 (t0) cc_final: 0.6892 (t0) REVERT: W 924 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7989 (mm-30) outliers start: 32 outliers final: 17 residues processed: 338 average time/residue: 0.3985 time to fit residues: 184.3662 Evaluate side-chains 345 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 323 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 60 LEU 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 410 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 584 LEU Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 651 LYS Chi-restraints excluded: chain W residue 710 VAL Chi-restraints excluded: chain W residue 759 CYS Chi-restraints excluded: chain W residue 816 MET Chi-restraints excluded: chain W residue 824 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 152 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 675 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115313 restraints weight = 27371.821| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.54 r_work: 0.3237 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18996 Z= 0.175 Angle : 0.573 11.158 26995 Z= 0.334 Chirality : 0.037 0.205 3014 Planarity : 0.004 0.040 2320 Dihedral : 29.424 176.992 5044 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.05 % Allowed : 15.74 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1395 helix: 2.09 (0.18), residues: 838 sheet: 0.01 (0.60), residues: 66 loop : -0.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 491 HIS 0.007 0.001 HIS W 385 PHE 0.032 0.002 PHE W 433 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 975) hydrogen bonds : angle 3.29714 ( 2506) covalent geometry : bond 0.00391 (18993) covalent geometry : angle 0.57308 (26995) Misc. bond : bond 0.00064 ( 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 336 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 311 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7737 (ttp80) REVERT: A 72 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.8343 (mtt-85) REVERT: B 78 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: B 92 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7960 (mtp85) REVERT: C 65 LEU cc_start: 0.8587 (mt) cc_final: 0.8220 (mp) REVERT: C 77 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8207 (mtt180) REVERT: D 31 LYS cc_start: 0.8263 (pptt) cc_final: 0.7877 (pptt) REVERT: D 56 MET cc_start: 0.7921 (tpp) cc_final: 0.7663 (tpp) REVERT: H 56 MET cc_start: 0.8332 (tpp) cc_final: 0.7802 (tpt) REVERT: W 302 ASP cc_start: 0.6585 (t0) cc_final: 0.4417 (m-30) REVERT: W 318 TYR cc_start: 0.6785 (t80) cc_final: 0.6478 (t80) REVERT: W 339 LYS cc_start: 0.8512 (mttt) cc_final: 0.8188 (mtmm) REVERT: W 385 HIS cc_start: 0.7974 (m170) cc_final: 0.7716 (m90) REVERT: W 386 LYS cc_start: 0.8454 (mtmt) cc_final: 0.7970 (mtmm) REVERT: W 387 GLN cc_start: 0.8156 (mt0) cc_final: 0.7710 (mt0) REVERT: W 389 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7874 (mm-40) REVERT: W 412 LYS cc_start: 0.7842 (tptp) cc_final: 0.7439 (tptt) REVERT: W 416 LEU cc_start: 0.7968 (mt) cc_final: 0.7643 (mp) REVERT: W 437 ILE cc_start: 0.8399 (mp) cc_final: 0.7867 (tp) REVERT: W 485 GLN cc_start: 0.8150 (mt0) cc_final: 0.7780 (mt0) REVERT: W 498 LYS cc_start: 0.7748 (mttt) cc_final: 0.7509 (mttt) REVERT: W 507 GLU cc_start: 0.7978 (tt0) cc_final: 0.7723 (tt0) REVERT: W 526 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7178 (mt-10) REVERT: W 608 TRP cc_start: 0.7845 (m100) cc_final: 0.7519 (m100) REVERT: W 611 ILE cc_start: 0.8280 (mt) cc_final: 0.7928 (pt) REVERT: W 613 VAL cc_start: 0.8553 (t) cc_final: 0.8234 (m) REVERT: W 628 LYS cc_start: 0.8475 (mttt) cc_final: 0.8032 (ttmm) REVERT: W 651 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7499 (mttm) REVERT: W 661 MET cc_start: 0.7273 (mmm) cc_final: 0.6895 (mmm) REVERT: W 691 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6948 (tm-30) REVERT: W 700 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8371 (mtmm) REVERT: W 712 GLN cc_start: 0.7612 (pm20) cc_final: 0.7203 (pm20) REVERT: W 719 SER cc_start: 0.6848 (t) cc_final: 0.6557 (p) REVERT: W 729 ILE cc_start: 0.7908 (mt) cc_final: 0.7623 (tt) REVERT: W 734 TYR cc_start: 0.7741 (m-80) cc_final: 0.7461 (m-80) REVERT: W 735 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7431 (mmtp) REVERT: W 756 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7453 (mtpp) REVERT: W 757 LYS cc_start: 0.7687 (mttt) cc_final: 0.7045 (mmmm) REVERT: W 795 LYS cc_start: 0.8415 (mttt) cc_final: 0.8138 (mttt) REVERT: W 810 PHE cc_start: 0.7584 (m-80) cc_final: 0.7224 (m-80) REVERT: W 822 GLU cc_start: 0.7897 (tp30) cc_final: 0.7159 (tp30) REVERT: W 832 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7322 (mm-40) REVERT: W 839 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7307 (mmtt) REVERT: W 869 LEU cc_start: 0.7319 (mp) cc_final: 0.7048 (tt) REVERT: W 877 ASP cc_start: 0.7410 (m-30) cc_final: 0.7079 (m-30) REVERT: W 885 ASP cc_start: 0.7681 (t0) cc_final: 0.7348 (m-30) REVERT: W 909 ILE cc_start: 0.8173 (mp) cc_final: 0.7806 (mt) REVERT: W 919 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6862 (mt-10) REVERT: W 921 ASP cc_start: 0.7219 (t0) cc_final: 0.6794 (t0) REVERT: W 924 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7970 (mm-30) outliers start: 25 outliers final: 16 residues processed: 319 average time/residue: 0.3912 time to fit residues: 171.7708 Evaluate side-chains 327 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 49 THR 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 584 LEU Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 650 LEU Chi-restraints excluded: chain W residue 651 LYS Chi-restraints excluded: chain W residue 674 GLU 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 54 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 127 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 160 optimal weight: 0.2980 chunk 103 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112475 restraints weight = 27159.665| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.55 r_work: 0.3195 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 18996 Z= 0.272 Angle : 0.629 8.933 26995 Z= 0.361 Chirality : 0.042 0.189 3014 Planarity : 0.005 0.047 2320 Dihedral : 29.419 174.449 5044 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 15.82 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1395 helix: 1.98 (0.18), residues: 829 sheet: -0.07 (0.61), residues: 66 loop : -0.36 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP W 491 HIS 0.005 0.001 HIS W 385 PHE 0.027 0.002 PHE W 671 TYR 0.017 0.001 TYR W 410 ARG 0.008 0.000 ARG W 827 Details of bonding type rmsd hydrogen bonds : bond 0.04898 ( 975) hydrogen bonds : angle 3.43629 ( 2506) covalent geometry : bond 0.00617 (18993) covalent geometry : angle 0.62883 (26995) Misc. bond : bond 0.00088 ( 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 345 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8127 (ttp80) cc_final: 0.7732 (ttp80) REVERT: B 92 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8064 (mtp85) REVERT: C 77 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8210 (mtt180) REVERT: D 31 LYS cc_start: 0.8250 (pptt) cc_final: 0.7882 (pptt) REVERT: D 56 MET cc_start: 0.7997 (tpp) cc_final: 0.7673 (tpp) REVERT: D 90 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: F 85 ASP cc_start: 0.7847 (m-30) cc_final: 0.7571 (m-30) REVERT: H 56 MET cc_start: 0.8393 (tpp) cc_final: 0.7772 (tpt) REVERT: W 302 ASP cc_start: 0.6718 (t0) cc_final: 0.4520 (m-30) REVERT: W 318 TYR cc_start: 0.6923 (t80) cc_final: 0.6468 (t80) REVERT: W 339 LYS cc_start: 0.8489 (mttt) cc_final: 0.8255 (mttt) REVERT: W 385 HIS cc_start: 0.7966 (m170) cc_final: 0.7669 (m90) REVERT: W 386 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7985 (mtmm) REVERT: W 387 GLN cc_start: 0.8204 (mt0) cc_final: 0.7757 (mt0) REVERT: W 389 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7876 (mm-40) REVERT: W 393 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.7233 (ttt-90) REVERT: W 412 LYS cc_start: 0.7813 (tptp) cc_final: 0.7251 (tptt) REVERT: W 416 LEU cc_start: 0.8092 (mt) cc_final: 0.7655 (mp) REVERT: W 437 ILE cc_start: 0.8535 (mp) cc_final: 0.7972 (tp) REVERT: W 443 ARG cc_start: 0.8005 (ptm-80) cc_final: 0.6842 (ptm-80) REVERT: W 485 GLN cc_start: 0.8192 (mt0) cc_final: 0.7834 (mt0) REVERT: W 492 LEU cc_start: 0.8488 (mt) cc_final: 0.8084 (mt) REVERT: W 498 LYS cc_start: 0.7712 (mttt) cc_final: 0.7502 (mttt) REVERT: W 507 GLU cc_start: 0.7978 (tt0) cc_final: 0.7774 (tt0) REVERT: W 519 PHE cc_start: 0.8808 (t80) cc_final: 0.8606 (t80) REVERT: W 526 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7225 (mt-10) REVERT: W 557 ASN cc_start: 0.6566 (m-40) cc_final: 0.6320 (m-40) REVERT: W 575 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7008 (mt-10) REVERT: W 608 TRP cc_start: 0.7920 (m100) cc_final: 0.7545 (m100) REVERT: W 613 VAL cc_start: 0.8569 (t) cc_final: 0.8240 (m) REVERT: W 628 LYS cc_start: 0.8498 (mttt) cc_final: 0.8059 (ttmm) REVERT: W 661 MET cc_start: 0.7402 (mmm) cc_final: 0.7029 (mmm) REVERT: W 691 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7082 (tm-30) REVERT: W 699 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8306 (mtmt) REVERT: W 700 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8118 (ptpp) REVERT: W 703 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5419 (tm-30) REVERT: W 712 GLN cc_start: 0.7677 (pm20) cc_final: 0.7400 (pm20) REVERT: W 719 SER cc_start: 0.7064 (t) cc_final: 0.6780 (p) REVERT: W 729 ILE cc_start: 0.7961 (mt) cc_final: 0.7576 (tt) REVERT: W 735 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7483 (mmtp) REVERT: W 737 LEU cc_start: 0.7895 (mt) cc_final: 0.7691 (mp) REVERT: W 756 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7490 (mtpp) REVERT: W 757 LYS cc_start: 0.7885 (mttt) cc_final: 0.7159 (mmmm) REVERT: W 795 LYS cc_start: 0.8423 (mttt) cc_final: 0.8163 (mttt) REVERT: W 810 PHE cc_start: 0.7584 (m-80) cc_final: 0.7194 (m-80) REVERT: W 822 GLU cc_start: 0.7883 (tp30) cc_final: 0.7200 (tp30) REVERT: W 832 GLN cc_start: 0.7668 (mm110) cc_final: 0.7387 (mm110) REVERT: W 839 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7347 (mmtt) REVERT: W 877 ASP cc_start: 0.7440 (m-30) cc_final: 0.7138 (m-30) REVERT: W 909 ILE cc_start: 0.8150 (mp) cc_final: 0.7895 (mt) REVERT: W 919 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6910 (mt-10) REVERT: W 921 ASP cc_start: 0.7241 (t0) cc_final: 0.6815 (t0) REVERT: W 924 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8041 (mm-30) outliers start: 30 outliers final: 18 residues processed: 327 average time/residue: 0.3959 time to fit residues: 177.7701 Evaluate side-chains 329 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 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 410 TYR Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 584 LEU Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 650 LEU Chi-restraints excluded: chain W residue 651 LYS Chi-restraints excluded: chain W residue 664 LYS Chi-restraints excluded: chain W residue 816 MET 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 119 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112273 restraints weight = 27134.793| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.54 r_work: 0.3162 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18996 Z= 0.286 Angle : 0.635 9.396 26995 Z= 0.365 Chirality : 0.042 0.189 3014 Planarity : 0.005 0.085 2320 Dihedral : 29.482 175.894 5044 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.21 % Allowed : 16.48 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1395 helix: 1.80 (0.18), residues: 835 sheet: -0.04 (0.64), residues: 60 loop : -0.30 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP W 491 HIS 0.005 0.001 HIS W 849 PHE 0.032 0.002 PHE W 433 TYR 0.017 0.002 TYR W 410 ARG 0.005 0.000 ARG W 827 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 975) hydrogen bonds : angle 3.46551 ( 2506) covalent geometry : bond 0.00650 (18993) covalent geometry : angle 0.63454 (26995) Misc. bond : bond 0.00095 ( 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 342 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7688 (ttp80) REVERT: B 92 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: C 77 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8211 (mtt180) REVERT: D 31 LYS cc_start: 0.8258 (pptt) cc_final: 0.7875 (pptt) REVERT: D 56 MET cc_start: 0.7984 (tpp) cc_final: 0.7645 (tpp) REVERT: D 90 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: F 85 ASP cc_start: 0.7832 (m-30) cc_final: 0.7554 (m-30) REVERT: H 56 MET cc_start: 0.8399 (tpp) cc_final: 0.7672 (tpp) REVERT: W 302 ASP cc_start: 0.6794 (t0) cc_final: 0.4621 (m-30) REVERT: W 318 TYR cc_start: 0.6890 (t80) cc_final: 0.6451 (t80) REVERT: W 339 LYS cc_start: 0.8495 (mttt) cc_final: 0.8246 (mttt) REVERT: W 385 HIS cc_start: 0.7994 (m170) cc_final: 0.7672 (m90) REVERT: W 386 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7996 (mtmm) REVERT: W 387 GLN cc_start: 0.8229 (mt0) cc_final: 0.7809 (mt0) REVERT: W 389 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7881 (mm-40) REVERT: W 393 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.7227 (ttt-90) REVERT: W 412 LYS cc_start: 0.7820 (tptp) cc_final: 0.7311 (tptt) REVERT: W 416 LEU cc_start: 0.8029 (mt) cc_final: 0.7770 (mt) REVERT: W 437 ILE cc_start: 0.8556 (mp) cc_final: 0.8038 (tp) REVERT: W 443 ARG cc_start: 0.8059 (ptm-80) cc_final: 0.6899 (ptm-80) REVERT: W 485 GLN cc_start: 0.8210 (mt0) cc_final: 0.7794 (mt0) REVERT: W 492 LEU cc_start: 0.8456 (mt) cc_final: 0.8132 (mm) REVERT: W 498 LYS cc_start: 0.7738 (mttt) cc_final: 0.7497 (mttt) REVERT: W 507 GLU cc_start: 0.7946 (tt0) cc_final: 0.7707 (tt0) REVERT: W 526 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7236 (mp0) REVERT: W 557 ASN cc_start: 0.6684 (m-40) cc_final: 0.6445 (m-40) REVERT: W 560 VAL cc_start: 0.8899 (m) cc_final: 0.8599 (p) REVERT: W 575 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7034 (mt-10) REVERT: W 628 LYS cc_start: 0.8509 (mttt) cc_final: 0.8065 (ttmm) REVERT: W 651 LYS cc_start: 0.7946 (mttm) cc_final: 0.7626 (mttm) REVERT: W 661 MET cc_start: 0.7328 (mmm) cc_final: 0.6917 (mmm) REVERT: W 691 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7166 (tm-30) REVERT: W 699 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8276 (mtmt) REVERT: W 700 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8220 (ptpp) REVERT: W 712 GLN cc_start: 0.7731 (pm20) cc_final: 0.7526 (pm20) REVERT: W 719 SER cc_start: 0.7167 (t) cc_final: 0.6930 (p) REVERT: W 729 ILE cc_start: 0.7954 (mt) cc_final: 0.7572 (tt) REVERT: W 735 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7447 (mmtp) REVERT: W 756 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7468 (mtpp) REVERT: W 757 LYS cc_start: 0.7872 (mttt) cc_final: 0.7139 (mmmm) REVERT: W 795 LYS cc_start: 0.8429 (mttt) cc_final: 0.8202 (mttt) REVERT: W 803 ARG cc_start: 0.7922 (mmp80) cc_final: 0.7613 (mmp80) REVERT: W 807 VAL cc_start: 0.7788 (t) cc_final: 0.7371 (m) REVERT: W 810 PHE cc_start: 0.7581 (m-80) cc_final: 0.7166 (m-80) REVERT: W 812 GLN cc_start: 0.7033 (pt0) cc_final: 0.6766 (pt0) REVERT: W 822 GLU cc_start: 0.7903 (tp30) cc_final: 0.7288 (tp30) REVERT: W 832 GLN cc_start: 0.7554 (mm110) cc_final: 0.7316 (mm110) REVERT: W 839 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7346 (mmtt) REVERT: W 877 ASP cc_start: 0.7416 (m-30) cc_final: 0.7086 (m-30) REVERT: W 909 ILE cc_start: 0.8146 (mp) cc_final: 0.7912 (mt) REVERT: W 919 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6950 (mt-10) REVERT: W 921 ASP cc_start: 0.7266 (t0) cc_final: 0.6859 (t0) REVERT: W 924 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8084 (mm-30) outliers start: 27 outliers final: 20 residues processed: 327 average time/residue: 0.4157 time to fit residues: 187.1367 Evaluate side-chains 333 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 49 THR Chi-restraints excluded: chain H residue 87 THR 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 584 LEU Chi-restraints excluded: chain W residue 591 THR Chi-restraints excluded: chain W residue 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 650 LEU Chi-restraints excluded: chain W residue 764 LEU Chi-restraints excluded: chain W residue 816 MET 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 35 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 329 HIS W 828 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116305 restraints weight = 27406.365| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.55 r_work: 0.3233 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18996 Z= 0.165 Angle : 0.573 8.660 26995 Z= 0.331 Chirality : 0.036 0.193 3014 Planarity : 0.004 0.045 2320 Dihedral : 29.310 178.568 5044 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.56 % Allowed : 17.70 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1395 helix: 2.20 (0.18), residues: 835 sheet: 0.18 (0.66), residues: 55 loop : -0.21 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP W 491 HIS 0.004 0.001 HIS W 849 PHE 0.028 0.001 PHE W 433 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG W 803 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 975) hydrogen bonds : angle 3.24087 ( 2506) covalent geometry : bond 0.00367 (18993) covalent geometry : angle 0.57329 (26995) Misc. bond : bond 0.00068 ( 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 322 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7716 (ttp80) REVERT: B 92 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7987 (mtp85) REVERT: C 65 LEU cc_start: 0.8575 (mt) cc_final: 0.8351 (mp) REVERT: C 77 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (mtt180) REVERT: D 31 LYS cc_start: 0.8290 (pptt) cc_final: 0.7909 (pptt) REVERT: D 56 MET cc_start: 0.7867 (tpp) cc_final: 0.7611 (tpp) REVERT: W 302 ASP cc_start: 0.6789 (t0) cc_final: 0.4629 (m-30) REVERT: W 318 TYR cc_start: 0.6891 (t80) cc_final: 0.6371 (t80) REVERT: W 339 LYS cc_start: 0.8476 (mttt) cc_final: 0.8234 (mtmm) REVERT: W 385 HIS cc_start: 0.7947 (m170) cc_final: 0.7628 (m90) REVERT: W 387 GLN cc_start: 0.8197 (mt0) cc_final: 0.7774 (mt0) REVERT: W 389 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7924 (mm-40) REVERT: W 393 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7195 (ttt180) REVERT: W 412 LYS cc_start: 0.7853 (tptp) cc_final: 0.7306 (tptt) REVERT: W 437 ILE cc_start: 0.8487 (mp) cc_final: 0.7958 (tp) REVERT: W 443 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.6940 (ptm-80) REVERT: W 485 GLN cc_start: 0.7990 (mt0) cc_final: 0.7724 (mt0) REVERT: W 498 LYS cc_start: 0.7733 (mttt) cc_final: 0.7444 (mttt) REVERT: W 507 GLU cc_start: 0.7943 (tt0) cc_final: 0.7671 (tt0) REVERT: W 512 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7582 (mtmm) REVERT: W 526 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7310 (mp0) REVERT: W 557 ASN cc_start: 0.6595 (m-40) cc_final: 0.6355 (m-40) REVERT: W 560 VAL cc_start: 0.8877 (m) cc_final: 0.8559 (p) REVERT: W 561 TYR cc_start: 0.8690 (t80) cc_final: 0.8342 (t80) REVERT: W 611 ILE cc_start: 0.8211 (mt) cc_final: 0.7975 (mt) REVERT: W 628 LYS cc_start: 0.8497 (mttt) cc_final: 0.8088 (ttmm) REVERT: W 651 LYS cc_start: 0.7888 (mttm) cc_final: 0.7557 (mttm) REVERT: W 661 MET cc_start: 0.7251 (mmm) cc_final: 0.6843 (mmm) REVERT: W 691 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6971 (tm-30) REVERT: W 700 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8508 (mtmm) REVERT: W 712 GLN cc_start: 0.7645 (pm20) cc_final: 0.7345 (pm20) REVERT: W 719 SER cc_start: 0.6706 (t) cc_final: 0.6472 (p) REVERT: W 729 ILE cc_start: 0.7849 (mt) cc_final: 0.7544 (tt) REVERT: W 735 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7416 (mmtp) REVERT: W 756 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7446 (mtpp) REVERT: W 757 LYS cc_start: 0.7680 (mttt) cc_final: 0.7068 (mmmm) REVERT: W 807 VAL cc_start: 0.7724 (t) cc_final: 0.7405 (p) REVERT: W 810 PHE cc_start: 0.7571 (m-80) cc_final: 0.7185 (m-80) REVERT: W 812 GLN cc_start: 0.6931 (pt0) cc_final: 0.6666 (pt0) REVERT: W 822 GLU cc_start: 0.7847 (tp30) cc_final: 0.7238 (tp30) REVERT: W 832 GLN cc_start: 0.7466 (mm110) cc_final: 0.7243 (mm110) REVERT: W 839 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7380 (mmmt) REVERT: W 877 ASP cc_start: 0.7342 (m-30) cc_final: 0.7006 (m-30) REVERT: W 903 GLN cc_start: 0.8335 (mm110) cc_final: 0.7495 (tp-100) REVERT: W 919 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6914 (mt-10) REVERT: W 921 ASP cc_start: 0.7202 (t0) cc_final: 0.6743 (t0) REVERT: W 924 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 19 outliers final: 15 residues processed: 313 average time/residue: 0.4010 time to fit residues: 171.9104 Evaluate side-chains 316 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 299 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 87 THR 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 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 650 LEU Chi-restraints excluded: chain W residue 828 GLN 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 54 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115574 restraints weight = 27269.479| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.55 r_work: 0.3244 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18996 Z= 0.185 Angle : 0.589 10.015 26995 Z= 0.336 Chirality : 0.037 0.192 3014 Planarity : 0.004 0.043 2320 Dihedral : 29.273 177.635 5044 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.39 % Allowed : 18.36 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1395 helix: 2.20 (0.18), residues: 834 sheet: 0.15 (0.65), residues: 55 loop : -0.26 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP W 491 HIS 0.004 0.001 HIS W 849 PHE 0.029 0.002 PHE W 433 TYR 0.012 0.001 TYR D 80 ARG 0.011 0.000 ARG W 897 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 975) hydrogen bonds : angle 3.30048 ( 2506) covalent geometry : bond 0.00415 (18993) covalent geometry : angle 0.58880 (26995) Misc. bond : bond 0.00066 ( 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 325 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 308 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7737 (ttp80) REVERT: B 92 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7959 (mtp85) REVERT: C 65 LEU cc_start: 0.8574 (mt) cc_final: 0.8354 (mp) REVERT: C 77 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8241 (mtt180) REVERT: D 31 LYS cc_start: 0.8279 (pptt) cc_final: 0.7909 (pptt) REVERT: D 56 MET cc_start: 0.7932 (tpp) cc_final: 0.7658 (tpp) REVERT: H 56 MET cc_start: 0.8385 (tpp) cc_final: 0.7517 (tpp) REVERT: W 302 ASP cc_start: 0.6802 (t0) cc_final: 0.4625 (m-30) REVERT: W 318 TYR cc_start: 0.6876 (t80) cc_final: 0.6386 (t80) REVERT: W 339 LYS cc_start: 0.8472 (mttt) cc_final: 0.8223 (mttt) REVERT: W 385 HIS cc_start: 0.7959 (m170) cc_final: 0.7621 (m90) REVERT: W 386 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7943 (mtmm) REVERT: W 387 GLN cc_start: 0.8198 (mt0) cc_final: 0.7783 (mt0) REVERT: W 389 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7929 (mm-40) REVERT: W 393 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.7387 (ttt-90) REVERT: W 412 LYS cc_start: 0.7824 (tptp) cc_final: 0.7372 (tptt) REVERT: W 437 ILE cc_start: 0.8512 (mp) cc_final: 0.7981 (tp) REVERT: W 443 ARG cc_start: 0.8065 (ptm-80) cc_final: 0.6921 (ptm-80) REVERT: W 485 GLN cc_start: 0.7986 (mt0) cc_final: 0.7643 (mt0) REVERT: W 498 LYS cc_start: 0.7726 (mttt) cc_final: 0.7431 (mttt) REVERT: W 507 GLU cc_start: 0.7975 (tt0) cc_final: 0.7678 (tt0) REVERT: W 512 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7418 (mtmm) REVERT: W 526 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7114 (mp0) REVERT: W 557 ASN cc_start: 0.6618 (m-40) cc_final: 0.6384 (m-40) REVERT: W 560 VAL cc_start: 0.8886 (m) cc_final: 0.8576 (p) REVERT: W 628 LYS cc_start: 0.8505 (mttt) cc_final: 0.8097 (ttmm) REVERT: W 651 LYS cc_start: 0.7889 (mttm) cc_final: 0.7571 (mttm) REVERT: W 661 MET cc_start: 0.7275 (mmm) cc_final: 0.6845 (mmm) REVERT: W 664 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7820 (mmtt) REVERT: W 691 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7027 (tm-30) REVERT: W 700 LYS cc_start: 0.8873 (mtmm) cc_final: 0.8518 (mtmm) REVERT: W 712 GLN cc_start: 0.7693 (pm20) cc_final: 0.7393 (pm20) REVERT: W 719 SER cc_start: 0.6809 (t) cc_final: 0.6582 (p) REVERT: W 729 ILE cc_start: 0.7897 (mt) cc_final: 0.7562 (tt) REVERT: W 735 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7390 (mmtp) REVERT: W 756 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7455 (mtpp) REVERT: W 757 LYS cc_start: 0.7738 (mttt) cc_final: 0.7078 (mmmm) REVERT: W 807 VAL cc_start: 0.7693 (t) cc_final: 0.7374 (p) REVERT: W 810 PHE cc_start: 0.7596 (m-80) cc_final: 0.7223 (m-80) REVERT: W 812 GLN cc_start: 0.6906 (pt0) cc_final: 0.6646 (pt0) REVERT: W 822 GLU cc_start: 0.7821 (tp30) cc_final: 0.7199 (tp30) REVERT: W 832 GLN cc_start: 0.7474 (mm110) cc_final: 0.7256 (mm110) REVERT: W 839 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7402 (mmmt) REVERT: W 877 ASP cc_start: 0.7350 (m-30) cc_final: 0.7019 (m-30) REVERT: W 903 GLN cc_start: 0.8332 (mm110) cc_final: 0.7523 (tp-100) REVERT: W 919 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6923 (mt-10) REVERT: W 921 ASP cc_start: 0.7213 (t0) cc_final: 0.6736 (t0) REVERT: W 924 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8009 (mm-30) outliers start: 17 outliers final: 14 residues processed: 316 average time/residue: 0.4061 time to fit residues: 177.1960 Evaluate side-chains 318 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 87 THR 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 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 650 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 27 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114426 restraints weight = 27338.921| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.55 r_work: 0.3224 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18996 Z= 0.204 Angle : 0.611 10.586 26995 Z= 0.346 Chirality : 0.038 0.220 3014 Planarity : 0.004 0.043 2320 Dihedral : 29.268 177.825 5044 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.48 % Allowed : 18.61 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1395 helix: 2.13 (0.18), residues: 831 sheet: 0.24 (0.62), residues: 60 loop : -0.32 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP W 491 HIS 0.005 0.001 HIS W 574 PHE 0.029 0.002 PHE W 433 TYR 0.014 0.001 TYR D 80 ARG 0.012 0.000 ARG W 583 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 975) hydrogen bonds : angle 3.35770 ( 2506) covalent geometry : bond 0.00461 (18993) covalent geometry : angle 0.61081 (26995) Misc. bond : bond 0.00063 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11058.27 seconds wall clock time: 191 minutes 0.29 seconds (11460.29 seconds total)