Starting phenix.real_space_refine on Sun Jun 15 18:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ear_47841/06_2025/9ear_47841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ear_47841/06_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_47841/06_2025/9ear_47841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ear_47841/06_2025/9ear_47841.map" model { file = "/net/cci-nas-00/data/ceres_data/9ear_47841/06_2025/9ear_47841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ear_47841/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.69, per 1000 atoms: 0.59 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: 4.98 Conformation dependent library (CDL) restraints added in 1.6 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: 7.66 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: 11.76 Time building geometry restraints manager: 5.80 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 50.590 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.040 ------------------------------------------------------------------------------- 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 : 1.552 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: 0.4444 time to fit residues: 178.7040 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 : 1.474 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115001 restraints weight = 27632.193| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.55 r_work: 0.3237 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7696 (ttp80) REVERT: A 63 ARG cc_start: 0.7460 (mmp80) cc_final: 0.6911 (mmp80) REVERT: C 77 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8229 (mtt90) REVERT: D 31 LYS cc_start: 0.8115 (pptt) cc_final: 0.7789 (pptt) REVERT: D 43 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8129 (mmmm) REVERT: D 59 MET cc_start: 0.7928 (mmm) cc_final: 0.7699 (mmp) REVERT: D 118 TYR cc_start: 0.8464 (t80) cc_final: 0.7957 (t80) REVERT: E 63 ARG cc_start: 0.8467 (mmp80) cc_final: 0.8174 (mmp80) REVERT: H 56 MET cc_start: 0.8325 (tpp) cc_final: 0.8020 (tmm) REVERT: W 317 GLN cc_start: 0.5237 (mp10) cc_final: 0.4902 (mt0) REVERT: W 339 LYS cc_start: 0.8484 (mttt) cc_final: 0.8178 (mttt) REVERT: W 412 LYS cc_start: 0.7981 (tptt) cc_final: 0.7515 (tptt) REVERT: W 416 LEU cc_start: 0.7935 (mt) cc_final: 0.7611 (mp) REVERT: W 434 GLN cc_start: 0.7649 (tp-100) cc_final: 0.7325 (tp40) REVERT: W 437 ILE cc_start: 0.8420 (mp) cc_final: 0.7880 (tp) REVERT: W 485 GLN cc_start: 0.8193 (mt0) cc_final: 0.7860 (mt0) REVERT: W 503 ILE cc_start: 0.8374 (mt) cc_final: 0.8124 (mm) REVERT: W 535 LEU cc_start: 0.8515 (mt) cc_final: 0.8206 (mp) REVERT: W 588 ILE cc_start: 0.8510 (mt) cc_final: 0.8296 (mt) REVERT: W 600 LYS cc_start: 0.8509 (pttt) cc_final: 0.8232 (pttt) REVERT: W 613 VAL cc_start: 0.8368 (t) cc_final: 0.8019 (p) REVERT: W 661 MET cc_start: 0.7012 (mmm) cc_final: 0.6791 (mmm) REVERT: W 697 ARG cc_start: 0.7594 (mpp80) cc_final: 0.6930 (mpp80) REVERT: W 700 LYS cc_start: 0.8420 (mtmm) cc_final: 0.8062 (mtmm) REVERT: W 718 MET cc_start: 0.6433 (mtm) cc_final: 0.6206 (mtm) REVERT: W 722 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: W 724 GLN cc_start: 0.7866 (tt0) cc_final: 0.7634 (tp40) REVERT: W 729 ILE cc_start: 0.7926 (mt) cc_final: 0.7614 (tt) REVERT: W 734 TYR cc_start: 0.7631 (m-80) cc_final: 0.7384 (m-80) REVERT: W 735 LYS cc_start: 0.7830 (mmtp) cc_final: 0.7394 (mmtp) REVERT: W 756 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7499 (mtpp) REVERT: W 757 LYS cc_start: 0.7893 (mttt) cc_final: 0.7158 (mmmm) REVERT: W 782 HIS cc_start: 0.7087 (t-90) cc_final: 0.6867 (t-170) REVERT: W 795 LYS cc_start: 0.8328 (mttt) cc_final: 0.8112 (mttt) REVERT: W 810 PHE cc_start: 0.7661 (m-80) cc_final: 0.7385 (m-80) REVERT: W 816 MET cc_start: 0.8178 (tpt) cc_final: 0.7776 (tmm) REVERT: W 822 GLU cc_start: 0.7835 (tp30) cc_final: 0.7068 (tp30) REVERT: W 826 TYR cc_start: 0.6823 (m-10) cc_final: 0.6377 (m-10) REVERT: W 832 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7080 (mm-40) REVERT: W 839 LYS cc_start: 0.7595 (mttt) cc_final: 0.7260 (mmtt) REVERT: W 849 HIS cc_start: 0.7919 (t-90) cc_final: 0.7613 (t-170) REVERT: W 863 SER cc_start: 0.8188 (t) cc_final: 0.7960 (t) REVERT: W 869 LEU cc_start: 0.7152 (mp) cc_final: 0.6741 (tt) REVERT: W 877 ASP cc_start: 0.7387 (m-30) cc_final: 0.7075 (m-30) REVERT: W 892 LEU cc_start: 0.8365 (tp) cc_final: 0.8076 (mm) REVERT: W 893 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7755 (tp-100) REVERT: W 903 GLN cc_start: 0.8390 (mm110) cc_final: 0.7193 (mm110) REVERT: W 919 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6763 (mt-10) REVERT: W 921 ASP cc_start: 0.7266 (t0) cc_final: 0.6926 (t0) outliers start: 22 outliers final: 13 residues processed: 316 average time/residue: 0.4208 time to fit residues: 181.3037 Evaluate side-chains 322 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 307 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 145 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 chunk 128 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115724 restraints weight = 27414.339| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.55 r_work: 0.3246 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2431 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= 0.187 Angle : 0.588 9.006 26995 Z= 0.342 Chirality : 0.038 0.212 3014 Planarity : 0.004 0.039 2320 Dihedral : 29.396 175.047 5044 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.72 % Allowed : 12.38 % Favored : 85.90 % 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: 1.95 (0.23), residues: 1395 helix: 2.30 (0.18), residues: 828 sheet: -0.09 (0.62), residues: 65 loop : -0.21 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP W 491 HIS 0.004 0.001 HIS W 385 PHE 0.016 0.002 PHE W 671 TYR 0.010 0.001 TYR W 388 ARG 0.006 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 975) hydrogen bonds : angle 3.36161 ( 2506) covalent geometry : bond 0.00419 (18993) covalent geometry : angle 0.58806 (26995) Misc. bond : bond 0.00069 ( 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 324 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 303 time to evaluate : 1.498 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: 0.8120 (ttp80) cc_final: 0.7710 (ttp80) REVERT: A 72 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8263 (mtt-85) REVERT: B 92 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7930 (mtp85) REVERT: C 65 LEU cc_start: 0.8583 (mt) cc_final: 0.8364 (mp) REVERT: C 77 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8171 (mtt180) REVERT: D 31 LYS cc_start: 0.8162 (pptt) cc_final: 0.7804 (pptt) REVERT: D 56 MET cc_start: 0.8096 (tpp) cc_final: 0.7763 (tmm) REVERT: D 59 MET cc_start: 0.7905 (mmm) cc_final: 0.7681 (mmp) REVERT: D 118 TYR cc_start: 0.8548 (t80) cc_final: 0.8182 (t80) REVERT: H 56 MET cc_start: 0.8327 (tpp) cc_final: 0.8040 (tmm) REVERT: W 317 GLN cc_start: 0.5420 (mp10) cc_final: 0.5124 (mt0) REVERT: W 339 LYS cc_start: 0.8533 (mttt) cc_final: 0.8325 (mttt) REVERT: W 385 HIS cc_start: 0.7893 (m170) cc_final: 0.7603 (m170) REVERT: W 386 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8115 (mtmt) REVERT: W 389 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7649 (mm-40) REVERT: W 412 LYS cc_start: 0.7982 (tptt) cc_final: 0.7780 (tptt) REVERT: W 416 LEU cc_start: 0.8049 (mt) cc_final: 0.7719 (mp) REVERT: W 433 PHE cc_start: 0.7992 (m-80) cc_final: 0.7770 (m-80) REVERT: W 434 GLN cc_start: 0.7463 (tp-100) cc_final: 0.6780 (tp-100) REVERT: W 437 ILE cc_start: 0.8425 (mp) cc_final: 0.7916 (tp) REVERT: W 485 GLN cc_start: 0.8282 (mt0) cc_final: 0.7908 (mt0) REVERT: W 496 TRP cc_start: 0.8436 (t60) cc_final: 0.8196 (t-100) REVERT: W 503 ILE cc_start: 0.8301 (mt) cc_final: 0.8039 (mm) REVERT: W 507 GLU cc_start: 0.8019 (tt0) cc_final: 0.7619 (tt0) REVERT: W 535 LEU cc_start: 0.8538 (mt) cc_final: 0.8226 (mp) REVERT: W 588 ILE cc_start: 0.8458 (mt) cc_final: 0.8247 (mt) REVERT: W 600 LYS cc_start: 0.8539 (pttt) cc_final: 0.8282 (pttt) REVERT: W 613 VAL cc_start: 0.8400 (t) cc_final: 0.8042 (p) REVERT: W 628 LYS cc_start: 0.8471 (mttt) cc_final: 0.7990 (ttmm) REVERT: W 651 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7445 (mttm) REVERT: W 661 MET cc_start: 0.7061 (mmm) cc_final: 0.6771 (mmm) REVERT: W 699 LYS cc_start: 0.8298 (mttt) cc_final: 0.7960 (mtpt) REVERT: W 710 VAL cc_start: 0.7802 (t) cc_final: 0.7480 (t) REVERT: W 729 ILE cc_start: 0.7859 (mt) cc_final: 0.7552 (tt) REVERT: W 734 TYR cc_start: 0.7587 (m-80) cc_final: 0.7379 (m-80) REVERT: W 735 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7455 (mmtp) REVERT: W 756 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7440 (mtpp) REVERT: W 757 LYS cc_start: 0.7784 (mttt) cc_final: 0.7036 (mmtp) REVERT: W 795 LYS cc_start: 0.8357 (mttt) cc_final: 0.8120 (mttt) REVERT: W 810 PHE cc_start: 0.7596 (m-80) cc_final: 0.7265 (m-80) REVERT: W 816 MET cc_start: 0.8162 (tpt) cc_final: 0.7885 (tmm) REVERT: W 822 GLU cc_start: 0.7883 (tp30) cc_final: 0.7149 (tp30) REVERT: W 826 TYR cc_start: 0.7037 (m-10) cc_final: 0.6511 (m-10) REVERT: W 849 HIS cc_start: 0.8010 (t-90) cc_final: 0.7702 (t-170) REVERT: W 863 SER cc_start: 0.8162 (t) cc_final: 0.7925 (t) REVERT: W 869 LEU cc_start: 0.7113 (mp) cc_final: 0.6700 (tt) REVERT: W 877 ASP cc_start: 0.7389 (m-30) cc_final: 0.7116 (m-30) REVERT: W 893 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7784 (tp-100) REVERT: W 919 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6797 (mt-10) REVERT: W 921 ASP cc_start: 0.7243 (t0) cc_final: 0.6832 (t0) outliers start: 21 outliers final: 14 residues processed: 311 average time/residue: 0.4127 time to fit residues: 176.6781 Evaluate side-chains 318 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 301 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 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: 0.6980 chunk 141 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- 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 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117460 restraints weight = 27321.439| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.55 r_work: 0.3268 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2882 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= 0.164 Angle : 0.563 11.410 26995 Z= 0.327 Chirality : 0.036 0.206 3014 Planarity : 0.004 0.038 2320 Dihedral : 29.248 173.745 5044 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.97 % Allowed : 13.28 % Favored : 84.75 % 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: 2.04 (0.23), residues: 1395 helix: 2.40 (0.18), residues: 831 sheet: -0.05 (0.61), residues: 65 loop : -0.25 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 491 HIS 0.004 0.001 HIS W 687 PHE 0.027 0.001 PHE W 671 TYR 0.011 0.001 TYR W 484 ARG 0.005 0.000 ARG W 696 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 975) hydrogen bonds : angle 3.20806 ( 2506) covalent geometry : bond 0.00365 (18993) covalent geometry : angle 0.56293 (26995) Misc. bond : bond 0.00049 ( 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 329 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 1.380 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: 0.8116 (ttp80) cc_final: 0.7714 (ttp80) REVERT: A 72 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8294 (mtt-85) REVERT: B 92 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7904 (mtp85) REVERT: C 65 LEU cc_start: 0.8589 (mt) cc_final: 0.8347 (mp) REVERT: C 77 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8237 (mtt180) REVERT: C 81 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7992 (tpt170) REVERT: D 31 LYS cc_start: 0.8214 (pptt) cc_final: 0.7848 (pptt) REVERT: D 59 MET cc_start: 0.7870 (mmm) cc_final: 0.7637 (mmp) REVERT: D 118 TYR cc_start: 0.8563 (t80) cc_final: 0.8308 (t80) REVERT: H 56 MET cc_start: 0.8298 (tpp) cc_final: 0.8021 (tmm) REVERT: W 317 GLN cc_start: 0.5514 (mp10) cc_final: 0.5157 (mt0) REVERT: W 339 LYS cc_start: 0.8504 (mttt) cc_final: 0.8274 (mtmm) REVERT: W 385 HIS cc_start: 0.7896 (m170) cc_final: 0.7626 (m170) REVERT: W 416 LEU cc_start: 0.8096 (mt) cc_final: 0.7789 (mp) REVERT: W 437 ILE cc_start: 0.8453 (mp) cc_final: 0.7968 (tp) REVERT: W 485 GLN cc_start: 0.8210 (mt0) cc_final: 0.7867 (mt0) REVERT: W 498 LYS cc_start: 0.7676 (mttt) cc_final: 0.7428 (mttt) REVERT: W 503 ILE cc_start: 0.8220 (mt) cc_final: 0.8012 (mm) REVERT: W 507 GLU cc_start: 0.8041 (tt0) cc_final: 0.7790 (tt0) REVERT: W 575 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7081 (mm-30) REVERT: W 588 ILE cc_start: 0.8449 (mt) cc_final: 0.8235 (mt) REVERT: W 600 LYS cc_start: 0.8544 (pttt) cc_final: 0.8284 (pttt) REVERT: W 613 VAL cc_start: 0.8433 (t) cc_final: 0.8098 (m) REVERT: W 628 LYS cc_start: 0.8477 (mttt) cc_final: 0.8013 (ttmm) REVERT: W 661 MET cc_start: 0.7155 (mmm) cc_final: 0.6841 (mmm) REVERT: W 700 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8214 (mtmm) REVERT: W 729 ILE cc_start: 0.7888 (mt) cc_final: 0.7611 (tt) REVERT: W 734 TYR cc_start: 0.7623 (m-80) cc_final: 0.7420 (m-80) REVERT: W 756 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7453 (mtpp) REVERT: W 757 LYS cc_start: 0.7747 (mttt) cc_final: 0.7075 (mmmm) REVERT: W 795 LYS cc_start: 0.8367 (mttt) cc_final: 0.8120 (mttt) REVERT: W 810 PHE cc_start: 0.7586 (m-80) cc_final: 0.7244 (m-80) REVERT: W 822 GLU cc_start: 0.7842 (tp30) cc_final: 0.7090 (tp30) REVERT: W 826 TYR cc_start: 0.7122 (m-10) cc_final: 0.6506 (m-10) REVERT: W 839 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7305 (mmmt) REVERT: W 848 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6902 (m-30) REVERT: W 849 HIS cc_start: 0.8029 (t-90) cc_final: 0.7732 (t-170) REVERT: W 869 LEU cc_start: 0.7141 (mp) cc_final: 0.6918 (tt) REVERT: W 877 ASP cc_start: 0.7377 (m-30) cc_final: 0.7123 (m-30) REVERT: W 893 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7862 (tp-100) REVERT: W 903 GLN cc_start: 0.8424 (mm110) cc_final: 0.7899 (mm110) REVERT: W 919 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6786 (mt-10) REVERT: W 921 ASP cc_start: 0.7218 (t0) cc_final: 0.6801 (t0) outliers start: 24 outliers final: 15 residues processed: 309 average time/residue: 0.4280 time to fit residues: 181.7195 Evaluate side-chains 323 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain W residue 477 GLU Chi-restraints excluded: chain W residue 530 TYR 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 Chi-restraints excluded: chain W residue 848 ASP Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 434 GLN ** W 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111285 restraints weight = 27422.236| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.57 r_work: 0.3176 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 18996 Z= 0.334 Angle : 0.661 11.257 26995 Z= 0.380 Chirality : 0.045 0.189 3014 Planarity : 0.005 0.050 2320 Dihedral : 29.462 173.705 5044 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.46 % Allowed : 13.61 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.22), residues: 1395 helix: 1.85 (0.18), residues: 838 sheet: 0.05 (0.61), residues: 66 loop : -0.47 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP W 491 HIS 0.005 0.001 HIS D 46 PHE 0.026 0.002 PHE W 671 TYR 0.014 0.002 TYR W 410 ARG 0.007 0.001 ARG W 697 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 975) hydrogen bonds : angle 3.55541 ( 2506) covalent geometry : bond 0.00759 (18993) covalent geometry : angle 0.66134 (26995) Misc. bond : bond 0.00104 ( 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 352 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 1.343 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: 0.8117 (ttp80) cc_final: 0.7698 (ttp80) REVERT: B 92 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8128 (mtp85) REVERT: C 77 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8120 (mtt180) REVERT: D 31 LYS cc_start: 0.8235 (pptt) cc_final: 0.7893 (pptt) REVERT: D 56 MET cc_start: 0.8072 (tpp) cc_final: 0.7729 (tpp) REVERT: D 90 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: F 85 ASP cc_start: 0.7885 (m-30) cc_final: 0.7632 (m-30) REVERT: H 56 MET cc_start: 0.8417 (tpp) cc_final: 0.7740 (tpt) REVERT: W 317 GLN cc_start: 0.5632 (mp10) cc_final: 0.5344 (mt0) REVERT: W 339 LYS cc_start: 0.8444 (mttt) cc_final: 0.8125 (mtmm) REVERT: W 385 HIS cc_start: 0.7999 (m170) cc_final: 0.7650 (m170) REVERT: W 387 GLN cc_start: 0.8125 (mt0) cc_final: 0.7698 (mt0) REVERT: W 389 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7887 (mm-40) REVERT: W 416 LEU cc_start: 0.8230 (mt) cc_final: 0.7965 (mp) REVERT: W 437 ILE cc_start: 0.8534 (mp) cc_final: 0.8043 (tp) REVERT: W 485 GLN cc_start: 0.8236 (mt0) cc_final: 0.7839 (mt0) REVERT: W 498 LYS cc_start: 0.7787 (mttt) cc_final: 0.7549 (mttt) REVERT: W 507 GLU cc_start: 0.8050 (tt0) cc_final: 0.7805 (tt0) REVERT: W 526 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7251 (mt-10) REVERT: W 588 ILE cc_start: 0.8473 (mt) cc_final: 0.8256 (mt) REVERT: W 599 ASP cc_start: 0.7577 (p0) cc_final: 0.7374 (p0) REVERT: W 600 LYS cc_start: 0.8591 (pttt) cc_final: 0.8350 (pttt) REVERT: W 613 VAL cc_start: 0.8540 (t) cc_final: 0.8214 (m) REVERT: W 628 LYS cc_start: 0.8554 (mttt) cc_final: 0.8084 (ttmm) REVERT: W 661 MET cc_start: 0.7343 (mmm) cc_final: 0.6967 (mmm) REVERT: W 691 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6930 (tm-30) REVERT: W 700 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8509 (mtmm) REVERT: W 719 SER cc_start: 0.7094 (t) cc_final: 0.6774 (p) REVERT: W 729 ILE cc_start: 0.7964 (mt) cc_final: 0.7569 (tt) REVERT: W 735 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7455 (mmtp) REVERT: W 756 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7499 (mtpp) REVERT: W 757 LYS cc_start: 0.7974 (mttt) cc_final: 0.7257 (mttm) REVERT: W 795 LYS cc_start: 0.8411 (mttt) cc_final: 0.8142 (mttt) REVERT: W 810 PHE cc_start: 0.7627 (m-80) cc_final: 0.7171 (m-80) REVERT: W 822 GLU cc_start: 0.7895 (tp30) cc_final: 0.7143 (tp30) REVERT: W 826 TYR cc_start: 0.7283 (m-10) cc_final: 0.6652 (m-10) REVERT: W 832 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7401 (mm-40) REVERT: W 839 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7391 (mmmt) REVERT: W 869 LEU cc_start: 0.7369 (mp) cc_final: 0.7057 (tt) REVERT: W 877 ASP cc_start: 0.7437 (m-30) cc_final: 0.7148 (m-30) REVERT: W 893 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7872 (tp-100) REVERT: W 903 GLN cc_start: 0.8445 (mm110) cc_final: 0.7644 (mm-40) REVERT: W 909 ILE cc_start: 0.8053 (mp) cc_final: 0.7719 (mt) REVERT: W 919 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6878 (mt-10) REVERT: W 921 ASP cc_start: 0.7253 (t0) cc_final: 0.6841 (t0) REVERT: W 924 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7933 (mm-30) outliers start: 30 outliers final: 19 residues processed: 333 average time/residue: 0.3997 time to fit residues: 183.0273 Evaluate side-chains 335 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 313 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 58 THR Chi-restraints excluded: chain E residue 59 GLU 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 674 GLU Chi-restraints excluded: chain W residue 710 VAL Chi-restraints excluded: chain W residue 759 CYS Chi-restraints excluded: chain W residue 892 LEU Chi-restraints excluded: chain W residue 913 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 152 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114324 restraints weight = 27324.820| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.55 r_work: 0.3226 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18996 Z= 0.203 Angle : 0.587 12.155 26995 Z= 0.341 Chirality : 0.038 0.194 3014 Planarity : 0.004 0.042 2320 Dihedral : 29.392 176.654 5044 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.05 % Allowed : 14.51 % Favored : 83.44 % 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: 1.76 (0.23), residues: 1395 helix: 2.15 (0.18), residues: 829 sheet: 0.20 (0.60), residues: 65 loop : -0.36 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP W 491 HIS 0.003 0.001 HIS W 658 PHE 0.022 0.001 PHE W 671 TYR 0.012 0.001 TYR F 51 ARG 0.005 0.000 ARG W 697 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 975) hydrogen bonds : angle 3.29618 ( 2506) covalent geometry : bond 0.00457 (18993) covalent geometry : angle 0.58732 (26995) Misc. bond : bond 0.00077 ( 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 333 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 308 time to evaluate : 1.354 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: 0.8119 (ttp80) cc_final: 0.7723 (ttp80) REVERT: B 92 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7981 (mtp85) REVERT: C 77 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8172 (mtt180) REVERT: D 31 LYS cc_start: 0.8272 (pptt) cc_final: 0.7899 (pptt) REVERT: D 56 MET cc_start: 0.7994 (tpp) cc_final: 0.7700 (tpp) REVERT: F 85 ASP cc_start: 0.7822 (m-30) cc_final: 0.7548 (m-30) REVERT: H 56 MET cc_start: 0.8360 (tpp) cc_final: 0.7794 (tpt) REVERT: W 302 ASP cc_start: 0.6474 (t0) cc_final: 0.4177 (m-30) REVERT: W 317 GLN cc_start: 0.5649 (mp10) cc_final: 0.5283 (mt0) REVERT: W 339 LYS cc_start: 0.8494 (mttt) cc_final: 0.8232 (mtmm) REVERT: W 385 HIS cc_start: 0.7955 (m170) cc_final: 0.7559 (m170) REVERT: W 386 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7932 (mtmm) REVERT: W 387 GLN cc_start: 0.8131 (mt0) cc_final: 0.7667 (mt0) REVERT: W 389 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7885 (mm-40) REVERT: W 416 LEU cc_start: 0.8091 (mt) cc_final: 0.7843 (mp) REVERT: W 437 ILE cc_start: 0.8484 (mp) cc_final: 0.8067 (tp) REVERT: W 485 GLN cc_start: 0.8190 (mt0) cc_final: 0.7829 (mt0) REVERT: W 492 LEU cc_start: 0.8443 (mt) cc_final: 0.8152 (mm) REVERT: W 498 LYS cc_start: 0.7746 (mttt) cc_final: 0.7507 (mttt) REVERT: W 526 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7181 (mt-10) REVERT: W 575 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6996 (mm-30) REVERT: W 600 LYS cc_start: 0.8602 (pttt) cc_final: 0.8323 (pttt) REVERT: W 613 VAL cc_start: 0.8536 (t) cc_final: 0.8226 (m) REVERT: W 621 ASN cc_start: 0.8116 (t0) cc_final: 0.7913 (t0) REVERT: W 628 LYS cc_start: 0.8469 (mttt) cc_final: 0.8044 (ttmm) REVERT: W 661 MET cc_start: 0.7297 (mmm) cc_final: 0.6922 (mmm) REVERT: W 691 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6875 (tm-30) REVERT: W 700 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8380 (mtmm) REVERT: W 719 SER cc_start: 0.6951 (t) cc_final: 0.6666 (p) REVERT: W 729 ILE cc_start: 0.7926 (mt) cc_final: 0.7565 (tt) REVERT: W 734 TYR cc_start: 0.7712 (m-80) cc_final: 0.7349 (m-80) REVERT: W 735 LYS cc_start: 0.7893 (mmtp) cc_final: 0.7421 (mmtp) REVERT: W 756 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7485 (mtpp) REVERT: W 757 LYS cc_start: 0.7786 (mttt) cc_final: 0.7123 (mmmm) REVERT: W 795 LYS cc_start: 0.8377 (mttt) cc_final: 0.8081 (mttt) REVERT: W 822 GLU cc_start: 0.7879 (tp30) cc_final: 0.7141 (tp30) REVERT: W 832 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7329 (mm-40) REVERT: W 839 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7397 (mmmt) REVERT: W 869 LEU cc_start: 0.7285 (mp) cc_final: 0.7031 (tt) REVERT: W 877 ASP cc_start: 0.7394 (m-30) cc_final: 0.7049 (m-30) REVERT: W 885 ASP cc_start: 0.7653 (t0) cc_final: 0.7346 (m-30) REVERT: W 893 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7961 (tp-100) REVERT: W 903 GLN cc_start: 0.8416 (mm110) cc_final: 0.7802 (tp40) REVERT: W 919 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6802 (mt-10) REVERT: W 921 ASP cc_start: 0.7244 (t0) cc_final: 0.6805 (t0) REVERT: W 924 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7942 (mm-30) outliers start: 25 outliers final: 18 residues processed: 317 average time/residue: 0.3963 time to fit residues: 173.3959 Evaluate side-chains 328 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 308 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 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 651 LYS Chi-restraints excluded: chain W residue 674 GLU Chi-restraints excluded: chain W residue 824 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 50.0000 chunk 127 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 chunk 166 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 136 optimal weight: 0.0010 chunk 69 optimal weight: 0.9980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN F 75 HIS ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 546 GLN W 557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115144 restraints weight = 27194.405| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.53 r_work: 0.3240 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3386 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= 0.192 Angle : 0.579 8.926 26995 Z= 0.336 Chirality : 0.037 0.198 3014 Planarity : 0.004 0.046 2320 Dihedral : 29.284 175.580 5044 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.21 % Allowed : 15.16 % Favored : 82.62 % 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: 1.85 (0.23), residues: 1395 helix: 2.21 (0.18), residues: 830 sheet: 0.13 (0.59), residues: 66 loop : -0.30 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP W 491 HIS 0.003 0.001 HIS B 75 PHE 0.034 0.002 PHE W 433 TYR 0.012 0.001 TYR F 51 ARG 0.010 0.000 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 975) hydrogen bonds : angle 3.27776 ( 2506) covalent geometry : bond 0.00431 (18993) covalent geometry : angle 0.57915 (26995) Misc. bond : bond 0.00081 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 2.147 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: 0.8109 (ttp80) cc_final: 0.7713 (ttp80) REVERT: B 92 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: C 77 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8232 (mtt180) REVERT: D 31 LYS cc_start: 0.8270 (pptt) cc_final: 0.7903 (pptt) REVERT: D 56 MET cc_start: 0.7968 (tpp) cc_final: 0.7665 (tpp) REVERT: W 302 ASP cc_start: 0.6552 (t0) cc_final: 0.4365 (m-30) REVERT: W 317 GLN cc_start: 0.5612 (mp10) cc_final: 0.5285 (mt0) REVERT: W 339 LYS cc_start: 0.8526 (mttt) cc_final: 0.8271 (mtmm) REVERT: W 386 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8033 (mtmm) REVERT: W 387 GLN cc_start: 0.8186 (mt0) cc_final: 0.7744 (mt0) REVERT: W 393 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7102 (ttt180) REVERT: W 412 LYS cc_start: 0.7816 (tptp) cc_final: 0.7439 (tptt) REVERT: W 416 LEU cc_start: 0.7981 (mt) cc_final: 0.7628 (mp) REVERT: W 437 ILE cc_start: 0.8518 (mp) cc_final: 0.8098 (tp) REVERT: W 485 GLN cc_start: 0.8143 (mt0) cc_final: 0.7766 (mt0) REVERT: W 492 LEU cc_start: 0.8408 (mt) cc_final: 0.8131 (mm) REVERT: W 498 LYS cc_start: 0.7694 (mttt) cc_final: 0.7436 (mttt) REVERT: W 507 GLU cc_start: 0.8083 (tt0) cc_final: 0.7780 (tt0) REVERT: W 526 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7142 (mt-10) REVERT: W 575 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6786 (mm-30) REVERT: W 600 LYS cc_start: 0.8554 (pttt) cc_final: 0.8280 (pttt) REVERT: W 608 TRP cc_start: 0.7879 (m100) cc_final: 0.7483 (m100) REVERT: W 613 VAL cc_start: 0.8528 (t) cc_final: 0.8190 (m) REVERT: W 621 ASN cc_start: 0.8111 (t0) cc_final: 0.7905 (t0) REVERT: W 628 LYS cc_start: 0.8492 (mttt) cc_final: 0.8083 (ttmm) REVERT: W 651 LYS cc_start: 0.7806 (mttm) cc_final: 0.7507 (mttm) REVERT: W 661 MET cc_start: 0.7342 (mmm) cc_final: 0.6943 (mmm) REVERT: W 691 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6979 (tm-30) REVERT: W 719 SER cc_start: 0.6955 (t) cc_final: 0.6679 (p) REVERT: W 729 ILE cc_start: 0.7925 (mt) cc_final: 0.7560 (tt) REVERT: W 734 TYR cc_start: 0.7718 (m-80) cc_final: 0.7381 (m-80) REVERT: W 735 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7462 (mmtp) REVERT: W 756 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7473 (mtpp) REVERT: W 757 LYS cc_start: 0.7753 (mttt) cc_final: 0.7084 (mmmm) REVERT: W 793 LEU cc_start: 0.7976 (tp) cc_final: 0.7390 (tt) REVERT: W 795 LYS cc_start: 0.8375 (mttt) cc_final: 0.8090 (mttt) REVERT: W 810 PHE cc_start: 0.7589 (m-80) cc_final: 0.7202 (m-80) REVERT: W 822 GLU cc_start: 0.7884 (tp30) cc_final: 0.7170 (tp30) REVERT: W 826 TYR cc_start: 0.7292 (m-10) cc_final: 0.6627 (m-10) REVERT: W 832 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7499 (mm-40) REVERT: W 839 LYS cc_start: 0.7609 (mmtt) cc_final: 0.7403 (mmmt) REVERT: W 869 LEU cc_start: 0.7336 (mp) cc_final: 0.7051 (tt) REVERT: W 877 ASP cc_start: 0.7368 (m-30) cc_final: 0.7080 (m-30) REVERT: W 885 ASP cc_start: 0.7683 (t0) cc_final: 0.7379 (m-30) REVERT: W 893 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7992 (tp-100) REVERT: W 903 GLN cc_start: 0.8391 (mm110) cc_final: 0.7744 (mm110) REVERT: W 919 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6838 (mt-10) REVERT: W 921 ASP cc_start: 0.7197 (t0) cc_final: 0.6734 (t0) REVERT: W 924 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7926 (mm-30) outliers start: 27 outliers final: 18 residues processed: 316 average time/residue: 0.4763 time to fit residues: 210.9128 Evaluate side-chains 321 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 301 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 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 824 LEU Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 161 optimal weight: 0.0670 chunk 148 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115150 restraints weight = 27093.490| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.54 r_work: 0.3235 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3527 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= 0.197 Angle : 0.581 9.213 26995 Z= 0.336 Chirality : 0.037 0.198 3014 Planarity : 0.004 0.061 2320 Dihedral : 29.259 175.804 5044 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.89 % Allowed : 16.39 % 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: 1.81 (0.23), residues: 1395 helix: 2.16 (0.18), residues: 835 sheet: 0.14 (0.62), residues: 60 loop : -0.30 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP W 491 HIS 0.010 0.001 HIS W 385 PHE 0.025 0.001 PHE W 671 TYR 0.012 0.001 TYR F 51 ARG 0.010 0.000 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 975) hydrogen bonds : angle 3.28839 ( 2506) covalent geometry : bond 0.00443 (18993) covalent geometry : angle 0.58131 (26995) Misc. bond : bond 0.00077 ( 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 328 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7708 (ttp80) REVERT: B 92 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7984 (mtp85) REVERT: C 77 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8198 (mtt180) REVERT: D 31 LYS cc_start: 0.8276 (pptt) cc_final: 0.7909 (pptt) REVERT: D 56 MET cc_start: 0.7970 (tpp) cc_final: 0.7667 (tpp) REVERT: H 56 MET cc_start: 0.8369 (tpp) cc_final: 0.7557 (tpp) REVERT: W 302 ASP cc_start: 0.6613 (t0) cc_final: 0.4416 (m-30) REVERT: W 339 LYS cc_start: 0.8526 (mttt) cc_final: 0.8261 (mtmm) REVERT: W 385 HIS cc_start: 0.8052 (m170) cc_final: 0.7769 (m90) REVERT: W 386 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7950 (mtmm) REVERT: W 387 GLN cc_start: 0.8167 (mt0) cc_final: 0.7681 (mt0) REVERT: W 389 GLN cc_start: 0.8469 (mm110) cc_final: 0.7709 (mm110) REVERT: W 393 ARG cc_start: 0.8076 (mtp-110) cc_final: 0.6855 (ttp-170) REVERT: W 412 LYS cc_start: 0.7846 (tptp) cc_final: 0.7434 (tptt) REVERT: W 416 LEU cc_start: 0.7964 (mt) cc_final: 0.7644 (mp) REVERT: W 437 ILE cc_start: 0.8482 (mp) cc_final: 0.8063 (tp) REVERT: W 485 GLN cc_start: 0.8144 (mt0) cc_final: 0.7844 (mt0) REVERT: W 492 LEU cc_start: 0.8327 (mt) cc_final: 0.8070 (mm) REVERT: W 498 LYS cc_start: 0.7596 (mttt) cc_final: 0.7334 (mttt) REVERT: W 526 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7134 (mt-10) REVERT: W 545 TRP cc_start: 0.8511 (m100) cc_final: 0.8117 (m100) REVERT: W 557 ASN cc_start: 0.6930 (t0) cc_final: 0.6714 (m-40) REVERT: W 575 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6613 (mm-30) REVERT: W 613 VAL cc_start: 0.8515 (t) cc_final: 0.8173 (m) REVERT: W 628 LYS cc_start: 0.8492 (mttt) cc_final: 0.8058 (ttmm) REVERT: W 661 MET cc_start: 0.7331 (mmm) cc_final: 0.6928 (mmm) REVERT: W 668 TRP cc_start: 0.7996 (t-100) cc_final: 0.7653 (t-100) REVERT: W 691 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7012 (tm-30) REVERT: W 719 SER cc_start: 0.6970 (t) cc_final: 0.6691 (p) REVERT: W 729 ILE cc_start: 0.7929 (mt) cc_final: 0.7555 (tt) REVERT: W 734 TYR cc_start: 0.7721 (m-80) cc_final: 0.7370 (m-80) REVERT: W 735 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7445 (mmtp) REVERT: W 756 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7486 (mtpp) REVERT: W 757 LYS cc_start: 0.7779 (mttt) cc_final: 0.6946 (mttm) REVERT: W 795 LYS cc_start: 0.8393 (mttt) cc_final: 0.8095 (mttt) REVERT: W 810 PHE cc_start: 0.7594 (m-80) cc_final: 0.7203 (m-80) REVERT: W 822 GLU cc_start: 0.7832 (tp30) cc_final: 0.7121 (tp30) REVERT: W 826 TYR cc_start: 0.7249 (m-10) cc_final: 0.6565 (m-10) REVERT: W 832 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7451 (mm-40) REVERT: W 877 ASP cc_start: 0.7385 (m-30) cc_final: 0.7102 (m-30) REVERT: W 885 ASP cc_start: 0.7699 (t0) cc_final: 0.7378 (m-30) REVERT: W 903 GLN cc_start: 0.8372 (mm110) cc_final: 0.7780 (tp40) REVERT: W 919 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6855 (mt-10) REVERT: W 921 ASP cc_start: 0.7221 (t0) cc_final: 0.6743 (t0) REVERT: W 924 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7936 (mm-30) outliers start: 23 outliers final: 19 residues processed: 317 average time/residue: 0.5604 time to fit residues: 251.6177 Evaluate side-chains 320 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 G residue 108 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 591 THR 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 764 LEU Chi-restraints excluded: chain W residue 824 LEU Chi-restraints excluded: chain W residue 873 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 138 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 578 HIS W 832 GLN W 893 GLN ** W 899 HIS ** 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 = 0.3904 r_free = 0.3904 target = 0.152652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117273 restraints weight = 27273.275| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.56 r_work: 0.3247 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3724 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= 0.158 Angle : 0.567 10.548 26995 Z= 0.328 Chirality : 0.036 0.200 3014 Planarity : 0.004 0.043 2320 Dihedral : 29.165 178.990 5044 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.64 % Allowed : 16.80 % Favored : 81.56 % 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: 1.98 (0.23), residues: 1395 helix: 2.32 (0.18), residues: 834 sheet: 0.27 (0.61), residues: 60 loop : -0.27 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP W 491 HIS 0.011 0.001 HIS W 385 PHE 0.033 0.001 PHE W 433 TYR 0.011 0.001 TYR D 80 ARG 0.011 0.000 ARG W 583 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 975) hydrogen bonds : angle 3.21143 ( 2506) covalent geometry : bond 0.00351 (18993) covalent geometry : angle 0.56700 (26995) Misc. bond : bond 0.00070 ( 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 318 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 298 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7749 (ttp80) REVERT: B 92 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7994 (mtp85) REVERT: C 77 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8249 (mtt180) REVERT: D 31 LYS cc_start: 0.8283 (pptt) cc_final: 0.7901 (pptt) REVERT: D 56 MET cc_start: 0.7938 (tpp) cc_final: 0.7668 (tpp) REVERT: H 56 MET cc_start: 0.8341 (tpp) cc_final: 0.7521 (tpp) REVERT: W 302 ASP cc_start: 0.6602 (t0) cc_final: 0.4382 (m-30) REVERT: W 339 LYS cc_start: 0.8524 (mttt) cc_final: 0.8246 (mtmm) REVERT: W 385 HIS cc_start: 0.7942 (m170) cc_final: 0.7635 (m90) REVERT: W 386 LYS cc_start: 0.8453 (mtmt) cc_final: 0.7930 (mtmm) REVERT: W 387 GLN cc_start: 0.8136 (mt0) cc_final: 0.7632 (mt0) REVERT: W 389 GLN cc_start: 0.8466 (mm110) cc_final: 0.7926 (mm110) REVERT: W 437 ILE cc_start: 0.8524 (mp) cc_final: 0.8104 (tp) REVERT: W 485 GLN cc_start: 0.8091 (mt0) cc_final: 0.7818 (mt0) REVERT: W 496 TRP cc_start: 0.8118 (t-100) cc_final: 0.7856 (t-100) REVERT: W 498 LYS cc_start: 0.7620 (mttt) cc_final: 0.7332 (mttt) REVERT: W 512 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7328 (mtmm) REVERT: W 526 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7010 (mt-10) REVERT: W 545 TRP cc_start: 0.8467 (m100) cc_final: 0.8013 (m100) REVERT: W 575 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6939 (mm-30) REVERT: W 628 LYS cc_start: 0.8494 (mttt) cc_final: 0.8093 (ttmm) REVERT: W 651 LYS cc_start: 0.7874 (mttm) cc_final: 0.7558 (mttm) REVERT: W 661 MET cc_start: 0.7246 (mmm) cc_final: 0.6912 (mmm) REVERT: W 691 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6946 (tm-30) REVERT: W 719 SER cc_start: 0.6886 (t) cc_final: 0.6662 (p) REVERT: W 729 ILE cc_start: 0.7831 (mt) cc_final: 0.7523 (tt) REVERT: W 734 TYR cc_start: 0.7688 (m-80) cc_final: 0.7329 (m-80) REVERT: W 735 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7440 (mmtp) REVERT: W 756 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7463 (mtpp) REVERT: W 757 LYS cc_start: 0.7687 (mttt) cc_final: 0.6986 (mttm) REVERT: W 793 LEU cc_start: 0.7950 (tp) cc_final: 0.7338 (tt) REVERT: W 795 LYS cc_start: 0.8370 (mttt) cc_final: 0.8067 (mttt) REVERT: W 810 PHE cc_start: 0.7593 (m-80) cc_final: 0.7215 (m-80) REVERT: W 822 GLU cc_start: 0.7832 (tp30) cc_final: 0.7096 (tp30) REVERT: W 839 LYS cc_start: 0.7558 (mmmt) cc_final: 0.7198 (mmmt) REVERT: W 877 ASP cc_start: 0.7367 (m-30) cc_final: 0.7079 (m-30) REVERT: W 885 ASP cc_start: 0.7694 (t70) cc_final: 0.7364 (m-30) REVERT: W 903 GLN cc_start: 0.8369 (mm110) cc_final: 0.7828 (tp-100) REVERT: W 919 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6874 (mt-10) REVERT: W 921 ASP cc_start: 0.7230 (t0) cc_final: 0.6739 (t0) REVERT: W 924 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7944 (mm-30) outliers start: 20 outliers final: 15 residues processed: 311 average time/residue: 0.4471 time to fit residues: 193.0567 Evaluate side-chains 313 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 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 764 LEU Chi-restraints excluded: chain W residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 109 optimal weight: 50.0000 chunk 130 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 578 HIS ** W 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116387 restraints weight = 27276.774| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.54 r_work: 0.3255 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18996 Z= 0.182 Angle : 0.578 11.848 26995 Z= 0.333 Chirality : 0.037 0.197 3014 Planarity : 0.004 0.041 2320 Dihedral : 29.146 176.540 5044 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 17.21 % 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: 1.92 (0.23), residues: 1395 helix: 2.26 (0.18), residues: 837 sheet: 0.22 (0.64), residues: 55 loop : -0.29 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP W 491 HIS 0.009 0.001 HIS W 385 PHE 0.031 0.002 PHE W 433 TYR 0.012 0.001 TYR D 80 ARG 0.010 0.000 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 975) hydrogen bonds : angle 3.25762 ( 2506) covalent geometry : bond 0.00410 (18993) covalent geometry : angle 0.57809 (26995) Misc. bond : bond 0.00053 ( 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 311 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7705 (ttp80) REVERT: B 92 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7979 (mtp85) REVERT: C 77 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8236 (mtt180) REVERT: D 31 LYS cc_start: 0.8284 (pptt) cc_final: 0.7920 (pptt) REVERT: D 56 MET cc_start: 0.7981 (tpp) cc_final: 0.7684 (tpp) REVERT: H 56 MET cc_start: 0.8364 (tpp) cc_final: 0.7523 (tpp) REVERT: W 302 ASP cc_start: 0.6644 (t0) cc_final: 0.4386 (m-30) REVERT: W 339 LYS cc_start: 0.8516 (mttt) cc_final: 0.8260 (mttt) REVERT: W 385 HIS cc_start: 0.7975 (m170) cc_final: 0.7658 (m90) REVERT: W 386 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7938 (mtmm) REVERT: W 387 GLN cc_start: 0.8179 (mt0) cc_final: 0.7705 (mt0) REVERT: W 389 GLN cc_start: 0.8463 (mm110) cc_final: 0.7906 (mm110) REVERT: W 412 LYS cc_start: 0.7975 (tptp) cc_final: 0.7671 (tptt) REVERT: W 437 ILE cc_start: 0.8519 (mp) cc_final: 0.8095 (tp) REVERT: W 485 GLN cc_start: 0.8049 (mt0) cc_final: 0.7807 (mt0) REVERT: W 496 TRP cc_start: 0.8136 (t-100) cc_final: 0.7879 (t-100) REVERT: W 498 LYS cc_start: 0.7697 (mttt) cc_final: 0.7410 (mttt) REVERT: W 526 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7077 (mt-10) REVERT: W 545 TRP cc_start: 0.8501 (m100) cc_final: 0.8084 (m100) REVERT: W 575 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6910 (mm-30) REVERT: W 611 ILE cc_start: 0.8133 (mt) cc_final: 0.7866 (mt) REVERT: W 628 LYS cc_start: 0.8496 (mttt) cc_final: 0.8095 (ttmm) REVERT: W 651 LYS cc_start: 0.7883 (mttm) cc_final: 0.7570 (mttm) REVERT: W 661 MET cc_start: 0.7239 (mmm) cc_final: 0.6913 (mmm) REVERT: W 691 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6972 (tm-30) REVERT: W 719 SER cc_start: 0.6913 (t) cc_final: 0.6703 (p) REVERT: W 729 ILE cc_start: 0.7903 (mt) cc_final: 0.7556 (tt) REVERT: W 735 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7435 (mmtp) REVERT: W 756 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7482 (mtpp) REVERT: W 757 LYS cc_start: 0.7755 (mttt) cc_final: 0.7095 (mmmm) REVERT: W 795 LYS cc_start: 0.8375 (mttt) cc_final: 0.8097 (mttt) REVERT: W 810 PHE cc_start: 0.7609 (m-80) cc_final: 0.7217 (m-80) REVERT: W 822 GLU cc_start: 0.7800 (tp30) cc_final: 0.7109 (tp30) REVERT: W 832 GLN cc_start: 0.7643 (mm110) cc_final: 0.7380 (mm110) REVERT: W 839 LYS cc_start: 0.7579 (mmmt) cc_final: 0.7221 (mmmt) REVERT: W 877 ASP cc_start: 0.7403 (m-30) cc_final: 0.7123 (m-30) REVERT: W 893 GLN cc_start: 0.8228 (tp40) cc_final: 0.7955 (tp40) REVERT: W 903 GLN cc_start: 0.8357 (mm110) cc_final: 0.7747 (tp40) REVERT: W 919 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6908 (mt-10) REVERT: W 921 ASP cc_start: 0.7220 (t0) cc_final: 0.6721 (t0) REVERT: W 924 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7940 (mm-30) outliers start: 18 outliers final: 16 residues processed: 304 average time/residue: 0.4859 time to fit residues: 207.5169 Evaluate side-chains 310 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 E residue 61 LEU Chi-restraints excluded: chain G residue 116 LEU 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 764 LEU Chi-restraints excluded: chain W residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 64 ASN B 75 HIS ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 899 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.147844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112513 restraints weight = 27181.669| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.54 r_work: 0.3195 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18996 Z= 0.285 Angle : 0.643 11.253 26995 Z= 0.369 Chirality : 0.043 0.192 3014 Planarity : 0.005 0.047 2320 Dihedral : 29.336 178.617 5044 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.64 % Allowed : 17.54 % Favored : 80.82 % 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: 1.55 (0.22), residues: 1395 helix: 1.94 (0.18), residues: 833 sheet: 0.28 (0.65), residues: 60 loop : -0.39 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP W 491 HIS 0.009 0.001 HIS W 385 PHE 0.033 0.002 PHE W 433 TYR 0.022 0.002 TYR F 98 ARG 0.011 0.001 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 975) hydrogen bonds : angle 3.46464 ( 2506) covalent geometry : bond 0.00646 (18993) covalent geometry : angle 0.64254 (26995) Misc. bond : bond 0.00084 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12824.85 seconds wall clock time: 228 minutes 18.81 seconds (13698.81 seconds total)