Starting phenix.real_space_refine on Thu Sep 18 14:52:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ear_47841/09_2025/9ear_47841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ear_47841/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ear_47841/09_2025/9ear_47841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ear_47841/09_2025/9ear_47841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ear_47841/09_2025/9ear_47841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ear_47841/09_2025/9ear_47841.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 318 5.49 5 S 36 5.16 5 Be 1 3.05 5 C 10367 2.51 5 N 3313 2.21 5 O 3966 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18004 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 845 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3219 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "J" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3259 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Chain: "W" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5460 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 17, 'TRANS': 645} Chain breaks: 3 Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.55, per 1000 atoms: 0.20 Number of scatterers: 18004 At special positions: 0 Unit cell: (97.94, 151.06, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 318 15.00 F 3 9.00 O 3966 8.00 N 3313 7.00 C 10367 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 502.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.80 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: 5.49 Time building geometry restraints manager: 1.99 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: 2.390 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 19.100 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.23), residues: 1395 helix: 1.95 (0.18), residues: 817 sheet: -0.18 (0.75), residues: 54 loop : -0.13 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 17 TYR 0.010 0.001 TYR W 410 PHE 0.009 0.001 PHE W 610 TRP 0.008 0.001 TRP W 552 HIS 0.004 0.001 HIS W 574 Details of bonding type rmsd covalent geometry : bond 0.00568 (18993) covalent geometry : angle 0.79101 (26995) hydrogen bonds : bond 0.12917 ( 975) hydrogen bonds : angle 5.06842 ( 2506) 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 : 0.496 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: 0.1860 time to fit residues: 74.7552 Evaluate side-chains 271 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 268 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain W residue 625 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.148742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113522 restraints weight = 27580.318| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.56 r_work: 0.3215 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18996 Z= 0.274 Angle : 0.664 9.841 26995 Z= 0.385 Chirality : 0.044 0.199 3014 Planarity : 0.005 0.040 2320 Dihedral : 29.631 174.352 5049 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.89 % Allowed : 9.84 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.23), residues: 1395 helix: 2.03 (0.18), residues: 829 sheet: -0.09 (0.71), residues: 54 loop : -0.30 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 88 TYR 0.011 0.002 TYR W 410 PHE 0.029 0.002 PHE W 533 TRP 0.026 0.002 TRP W 491 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00624 (18993) covalent geometry : angle 0.66428 (26995) hydrogen bonds : bond 0.05265 ( 975) hydrogen bonds : angle 3.58561 ( 2506) Misc. bond : bond 0.00123 ( 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 334 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A 72 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8326 (mtt-85) REVERT: B 78 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8216 (mtm-85) REVERT: C 77 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: D 31 LYS cc_start: 0.8092 (pptt) cc_final: 0.7761 (pptt) REVERT: D 43 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8116 (mmmm) REVERT: D 59 MET cc_start: 0.7975 (mmm) cc_final: 0.7761 (mmp) REVERT: D 118 TYR cc_start: 0.8475 (t80) cc_final: 0.7965 (t80) REVERT: F 85 ASP cc_start: 0.7859 (m-30) cc_final: 0.7591 (m-30) REVERT: H 56 MET cc_start: 0.8353 (tpp) cc_final: 0.8056 (tmm) REVERT: W 317 GLN cc_start: 0.5301 (mp10) cc_final: 0.4976 (mt0) REVERT: W 339 LYS cc_start: 0.8472 (mttt) cc_final: 0.8165 (mttt) REVERT: W 412 LYS cc_start: 0.7980 (tptt) cc_final: 0.7494 (tptt) REVERT: W 416 LEU cc_start: 0.8020 (mt) cc_final: 0.7657 (mp) REVERT: W 437 ILE cc_start: 0.8481 (mp) cc_final: 0.7902 (tp) REVERT: W 485 GLN cc_start: 0.8207 (mt0) cc_final: 0.7863 (mt0) REVERT: W 503 ILE cc_start: 0.8368 (mt) cc_final: 0.8118 (mm) REVERT: W 507 GLU cc_start: 0.7918 (tt0) cc_final: 0.7585 (tt0) REVERT: W 535 LEU cc_start: 0.8538 (mt) cc_final: 0.8216 (mp) REVERT: W 575 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7112 (mm-30) REVERT: W 588 ILE cc_start: 0.8521 (mt) cc_final: 0.8303 (mt) REVERT: W 600 LYS cc_start: 0.8535 (pttt) cc_final: 0.8265 (pttt) REVERT: W 613 VAL cc_start: 0.8397 (t) cc_final: 0.8093 (p) REVERT: W 634 LYS cc_start: 0.7501 (mttt) cc_final: 0.7281 (mttt) REVERT: W 651 LYS cc_start: 0.7892 (tttm) cc_final: 0.7633 (mttm) REVERT: W 661 MET cc_start: 0.7054 (mmm) cc_final: 0.6841 (mmm) REVERT: W 668 TRP cc_start: 0.7933 (t-100) cc_final: 0.7469 (t-100) REVERT: W 686 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7442 (mp) REVERT: W 697 ARG cc_start: 0.7734 (mpp80) cc_final: 0.7040 (mpp80) REVERT: W 700 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8126 (mtmm) REVERT: W 718 MET cc_start: 0.6532 (mtm) cc_final: 0.6312 (mtm) REVERT: W 722 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: W 724 GLN cc_start: 0.7884 (tt0) cc_final: 0.7642 (tp40) REVERT: W 729 ILE cc_start: 0.7938 (mt) cc_final: 0.7621 (tt) REVERT: W 734 TYR cc_start: 0.7637 (m-80) cc_final: 0.7414 (m-80) REVERT: W 735 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7393 (mmtp) REVERT: W 756 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7489 (mtpp) REVERT: W 757 LYS cc_start: 0.7956 (mttt) cc_final: 0.7196 (mmmm) REVERT: W 782 HIS cc_start: 0.7189 (t-90) cc_final: 0.6933 (t-170) REVERT: W 795 LYS cc_start: 0.8352 (mttt) cc_final: 0.8135 (mttt) REVERT: W 810 PHE cc_start: 0.7685 (m-80) cc_final: 0.7390 (m-80) REVERT: W 816 MET cc_start: 0.8194 (tpt) cc_final: 0.7846 (tmm) REVERT: W 822 GLU cc_start: 0.7831 (tp30) cc_final: 0.7095 (tp30) REVERT: W 826 TYR cc_start: 0.6976 (m-10) cc_final: 0.6553 (m-10) REVERT: W 832 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7151 (mm-40) REVERT: W 839 LYS cc_start: 0.7606 (mttt) cc_final: 0.7269 (mmtt) REVERT: W 844 LYS cc_start: 0.7992 (tttm) cc_final: 0.7633 (tttm) REVERT: W 849 HIS cc_start: 0.7948 (t-90) cc_final: 0.7666 (t-170) REVERT: W 863 SER cc_start: 0.8204 (t) cc_final: 0.7951 (t) REVERT: W 869 LEU cc_start: 0.7141 (mp) cc_final: 0.6606 (tt) REVERT: W 877 ASP cc_start: 0.7397 (m-30) cc_final: 0.7067 (m-30) REVERT: W 893 GLN cc_start: 0.8107 (tp-100) cc_final: 0.7792 (tp-100) REVERT: W 903 GLN cc_start: 0.8450 (mm110) cc_final: 0.7285 (mm110) REVERT: W 919 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6801 (mt-10) REVERT: W 921 ASP cc_start: 0.7260 (t0) cc_final: 0.6932 (t0) outliers start: 23 outliers final: 15 residues processed: 319 average time/residue: 0.1796 time to fit residues: 78.3714 Evaluate side-chains 327 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 309 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 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 625 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 686 LEU Chi-restraints excluded: chain W residue 722 GLN Chi-restraints excluded: chain W residue 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 73 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN E 108 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 781 GLN W 828 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113784 restraints weight = 27602.501| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.54 r_work: 0.3213 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18996 Z= 0.222 Angle : 0.602 9.008 26995 Z= 0.351 Chirality : 0.039 0.215 3014 Planarity : 0.004 0.040 2320 Dihedral : 29.463 173.806 5046 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.21 % Allowed : 12.46 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.22), residues: 1395 helix: 2.14 (0.18), residues: 828 sheet: -0.19 (0.61), residues: 65 loop : -0.32 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.013 0.001 TYR W 388 PHE 0.015 0.002 PHE W 277 TRP 0.031 0.002 TRP W 491 HIS 0.005 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00500 (18993) covalent geometry : angle 0.60186 (26995) hydrogen bonds : bond 0.04710 ( 975) hydrogen bonds : angle 3.42514 ( 2506) Misc. bond : bond 0.00074 ( 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 331 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7686 (ttp80) REVERT: A 72 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8294 (mtt-85) REVERT: B 78 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8149 (mtm-85) REVERT: B 92 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7958 (mtp85) REVERT: C 77 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8090 (mtt180) REVERT: C 81 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7875 (tpt170) REVERT: D 31 LYS cc_start: 0.8180 (pptt) cc_final: 0.7772 (pptt) REVERT: D 43 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8089 (mmmm) REVERT: D 56 MET cc_start: 0.8043 (tpp) cc_final: 0.7734 (tmm) REVERT: D 90 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: D 118 TYR cc_start: 0.8554 (t80) cc_final: 0.8309 (t80) REVERT: E 40 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7983 (ttt-90) REVERT: W 298 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7333 (pm20) REVERT: W 317 GLN cc_start: 0.5465 (mp10) cc_final: 0.4677 (mt0) REVERT: W 339 LYS cc_start: 0.8499 (mttt) cc_final: 0.8266 (mtmm) REVERT: W 412 LYS cc_start: 0.7979 (tptt) cc_final: 0.7533 (tptt) REVERT: W 416 LEU cc_start: 0.8134 (mt) cc_final: 0.7717 (mp) REVERT: W 437 ILE cc_start: 0.8522 (mp) cc_final: 0.7978 (tp) REVERT: W 485 GLN cc_start: 0.8287 (mt0) cc_final: 0.7890 (mt0) REVERT: W 496 TRP cc_start: 0.8425 (t60) cc_final: 0.8218 (t-100) REVERT: W 503 ILE cc_start: 0.8289 (mt) cc_final: 0.8026 (mm) REVERT: W 507 GLU cc_start: 0.8022 (tt0) cc_final: 0.7767 (tt0) REVERT: W 526 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7167 (mt-10) REVERT: W 573 THR cc_start: 0.7780 (p) cc_final: 0.7476 (t) REVERT: W 588 ILE cc_start: 0.8470 (mt) cc_final: 0.8250 (mt) REVERT: W 593 TYR cc_start: 0.7955 (m-80) cc_final: 0.7372 (m-10) REVERT: W 598 LYS cc_start: 0.7391 (mttm) cc_final: 0.7181 (mttm) REVERT: W 600 LYS cc_start: 0.8557 (pttt) cc_final: 0.8315 (pttt) REVERT: W 613 VAL cc_start: 0.8467 (t) cc_final: 0.8155 (m) REVERT: W 628 LYS cc_start: 0.8498 (mttt) cc_final: 0.8156 (ttmm) REVERT: W 651 LYS cc_start: 0.7864 (tttm) cc_final: 0.7637 (mttm) REVERT: W 661 MET cc_start: 0.7141 (mmm) cc_final: 0.6837 (mmm) REVERT: W 668 TRP cc_start: 0.8022 (t-100) cc_final: 0.7770 (t-100) REVERT: W 700 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8226 (mtmm) REVERT: W 718 MET cc_start: 0.6408 (mtm) cc_final: 0.6201 (mtm) REVERT: W 729 ILE cc_start: 0.7936 (mt) cc_final: 0.7634 (tt) REVERT: W 735 LYS cc_start: 0.7894 (mmtp) cc_final: 0.7447 (mmtp) REVERT: W 756 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7476 (mtpp) REVERT: W 757 LYS cc_start: 0.7857 (mttt) cc_final: 0.7181 (mmmm) REVERT: W 795 LYS cc_start: 0.8382 (mttt) cc_final: 0.8181 (mttt) REVERT: W 810 PHE cc_start: 0.7617 (m-80) cc_final: 0.7308 (m-80) REVERT: W 822 GLU cc_start: 0.7849 (tp30) cc_final: 0.7181 (tp30) REVERT: W 826 TYR cc_start: 0.7089 (m-10) cc_final: 0.6563 (m-10) REVERT: W 849 HIS cc_start: 0.7998 (t-90) cc_final: 0.7734 (t-170) REVERT: W 869 LEU cc_start: 0.7147 (mp) cc_final: 0.6775 (tt) REVERT: W 877 ASP cc_start: 0.7368 (m-30) cc_final: 0.7058 (m-30) REVERT: W 893 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7734 (tp-100) REVERT: W 903 GLN cc_start: 0.8423 (mm110) cc_final: 0.8012 (mm110) REVERT: W 919 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6863 (mt-10) REVERT: W 921 ASP cc_start: 0.7190 (t0) cc_final: 0.6812 (t0) outliers start: 27 outliers final: 16 residues processed: 313 average time/residue: 0.1789 time to fit residues: 76.3103 Evaluate side-chains 320 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 565 ILE Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 674 GLU Chi-restraints excluded: chain W residue 781 GLN Chi-restraints excluded: chain W residue 812 GLN Chi-restraints excluded: chain W residue 824 LEU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 330 ASN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113227 restraints weight = 27510.679| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.54 r_work: 0.3185 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18996 Z= 0.244 Angle : 0.612 9.317 26995 Z= 0.355 Chirality : 0.040 0.205 3014 Planarity : 0.004 0.044 2320 Dihedral : 29.461 173.451 5044 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.05 % Allowed : 13.11 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.22), residues: 1395 helix: 2.06 (0.18), residues: 830 sheet: -0.23 (0.61), residues: 65 loop : -0.42 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.012 0.001 TYR F 51 PHE 0.025 0.002 PHE W 671 TRP 0.043 0.002 TRP W 491 HIS 0.003 0.001 HIS W 658 Details of bonding type rmsd covalent geometry : bond 0.00552 (18993) covalent geometry : angle 0.61179 (26995) hydrogen bonds : bond 0.04831 ( 975) hydrogen bonds : angle 3.42530 ( 2506) Misc. bond : bond 0.00079 ( 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 340 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 315 time to evaluate : 0.463 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: 0.8123 (ttp80) cc_final: 0.7724 (ttp80) REVERT: B 78 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8130 (mtm-85) REVERT: B 92 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: C 77 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (mtt180) REVERT: C 81 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7866 (tpt170) REVERT: D 31 LYS cc_start: 0.8216 (pptt) cc_final: 0.7824 (pptt) REVERT: D 43 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8078 (mmmm) REVERT: F 85 ASP cc_start: 0.7835 (m-30) cc_final: 0.7538 (m-30) REVERT: H 56 MET cc_start: 0.8398 (tpp) cc_final: 0.8059 (tmm) REVERT: W 298 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7410 (pm20) REVERT: W 317 GLN cc_start: 0.5099 (mp10) cc_final: 0.4704 (mt0) REVERT: W 339 LYS cc_start: 0.8497 (mttt) cc_final: 0.8161 (mtmm) REVERT: W 352 TYR cc_start: 0.7643 (t80) cc_final: 0.7426 (t80) REVERT: W 387 GLN cc_start: 0.8114 (mt0) cc_final: 0.7672 (mt0) REVERT: W 393 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.6862 (ttt180) REVERT: W 412 LYS cc_start: 0.7967 (tptt) cc_final: 0.7520 (tptt) REVERT: W 416 LEU cc_start: 0.8192 (mt) cc_final: 0.7796 (mp) REVERT: W 432 LYS cc_start: 0.8054 (tppp) cc_final: 0.7744 (tppp) REVERT: W 433 PHE cc_start: 0.7965 (m-80) cc_final: 0.7680 (m-80) REVERT: W 437 ILE cc_start: 0.8465 (mp) cc_final: 0.7981 (tp) REVERT: W 485 GLN cc_start: 0.8271 (mt0) cc_final: 0.7922 (mt0) REVERT: W 498 LYS cc_start: 0.7761 (mttt) cc_final: 0.7532 (mttt) REVERT: W 503 ILE cc_start: 0.8235 (mt) cc_final: 0.8001 (mm) REVERT: W 507 GLU cc_start: 0.8022 (tt0) cc_final: 0.7815 (tt0) REVERT: W 526 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7430 (mp0) REVERT: W 561 TYR cc_start: 0.8784 (t80) cc_final: 0.8151 (t80) REVERT: W 575 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6527 (mm-30) REVERT: W 588 ILE cc_start: 0.8466 (mt) cc_final: 0.8237 (mt) REVERT: W 600 LYS cc_start: 0.8578 (pttt) cc_final: 0.8336 (pttt) REVERT: W 613 VAL cc_start: 0.8480 (t) cc_final: 0.8161 (m) REVERT: W 620 LYS cc_start: 0.7866 (pttt) cc_final: 0.6657 (ttpt) REVERT: W 628 LYS cc_start: 0.8521 (mttt) cc_final: 0.8033 (ttmm) REVERT: W 651 LYS cc_start: 0.7859 (tttm) cc_final: 0.7643 (mttm) REVERT: W 661 MET cc_start: 0.7253 (mmm) cc_final: 0.6908 (mmm) REVERT: W 700 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8019 (ptpp) REVERT: W 729 ILE cc_start: 0.7959 (mt) cc_final: 0.7560 (tt) REVERT: W 735 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7453 (mmtp) REVERT: W 756 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7539 (mtpp) REVERT: W 757 LYS cc_start: 0.7888 (mttt) cc_final: 0.7239 (mmmm) REVERT: W 781 GLN cc_start: 0.8237 (mt0) cc_final: 0.7989 (mt0) REVERT: W 795 LYS cc_start: 0.8405 (mttt) cc_final: 0.8157 (mttt) REVERT: W 810 PHE cc_start: 0.7608 (m-80) cc_final: 0.7201 (m-80) REVERT: W 822 GLU cc_start: 0.7892 (tp30) cc_final: 0.7287 (tp30) REVERT: W 828 GLN cc_start: 0.8020 (mp10) cc_final: 0.7503 (mp10) REVERT: W 839 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7340 (mmtt) REVERT: W 849 HIS cc_start: 0.8044 (t-90) cc_final: 0.7806 (t-170) REVERT: W 869 LEU cc_start: 0.7239 (mp) cc_final: 0.6925 (tt) REVERT: W 877 ASP cc_start: 0.7426 (m-30) cc_final: 0.7126 (m-30) REVERT: W 893 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7906 (tp-100) REVERT: W 903 GLN cc_start: 0.8455 (mm110) cc_final: 0.7994 (mm-40) REVERT: W 919 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6896 (mt-10) REVERT: W 921 ASP cc_start: 0.7230 (t0) cc_final: 0.6845 (t0) outliers start: 25 outliers final: 19 residues processed: 322 average time/residue: 0.1859 time to fit residues: 81.7302 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain W residue 391 VAL Chi-restraints excluded: chain W residue 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 639 LEU Chi-restraints excluded: chain W residue 642 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 136 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 40.0000 chunk 50 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 434 GLN W 469 GLN W 546 GLN W 675 HIS ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.112959 restraints weight = 27259.186| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.54 r_work: 0.3206 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18996 Z= 0.246 Angle : 0.611 9.823 26995 Z= 0.354 Chirality : 0.040 0.189 3014 Planarity : 0.004 0.046 2320 Dihedral : 29.464 173.981 5044 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.38 % Allowed : 13.85 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.22), residues: 1395 helix: 2.01 (0.18), residues: 833 sheet: -0.02 (0.62), residues: 65 loop : -0.49 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.013 0.001 TYR W 410 PHE 0.013 0.002 PHE D 67 TRP 0.054 0.002 TRP W 491 HIS 0.003 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00557 (18993) covalent geometry : angle 0.61055 (26995) hydrogen bonds : bond 0.04782 ( 975) hydrogen bonds : angle 3.43182 ( 2506) Misc. bond : bond 0.00079 ( 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 350 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 321 time to evaluate : 0.475 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: 0.8129 (ttp80) cc_final: 0.7738 (ttp80) REVERT: A 72 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8349 (mtt-85) REVERT: B 92 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8005 (mtp85) REVERT: C 77 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8219 (mtt180) REVERT: C 81 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7853 (tpt170) REVERT: D 31 LYS cc_start: 0.8264 (pptt) cc_final: 0.7896 (pptt) REVERT: D 43 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8056 (mmmm) REVERT: D 57 SER cc_start: 0.8806 (t) cc_final: 0.8568 (m) REVERT: F 85 ASP cc_start: 0.7829 (m-30) cc_final: 0.7534 (m-30) REVERT: W 302 ASP cc_start: 0.6501 (t0) cc_final: 0.4188 (m-30) REVERT: W 317 GLN cc_start: 0.5290 (mp10) cc_final: 0.4862 (mt0) REVERT: W 339 LYS cc_start: 0.8504 (mttt) cc_final: 0.8278 (mttt) REVERT: W 387 GLN cc_start: 0.8146 (mt0) cc_final: 0.7771 (mt0) REVERT: W 393 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.6913 (ttt180) REVERT: W 416 LEU cc_start: 0.8141 (mt) cc_final: 0.7827 (mp) REVERT: W 432 LYS cc_start: 0.8132 (tppp) cc_final: 0.7842 (tppp) REVERT: W 433 PHE cc_start: 0.7980 (m-80) cc_final: 0.7724 (m-80) REVERT: W 437 ILE cc_start: 0.8443 (mp) cc_final: 0.8090 (tp) REVERT: W 485 GLN cc_start: 0.8223 (mt0) cc_final: 0.7843 (mt0) REVERT: W 492 LEU cc_start: 0.8499 (mt) cc_final: 0.8296 (mt) REVERT: W 496 TRP cc_start: 0.8449 (t60) cc_final: 0.8197 (t-100) REVERT: W 498 LYS cc_start: 0.7728 (mttt) cc_final: 0.7498 (mttt) REVERT: W 503 ILE cc_start: 0.8202 (mt) cc_final: 0.7972 (mm) REVERT: W 526 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7228 (mt-10) REVERT: W 561 TYR cc_start: 0.8770 (t80) cc_final: 0.8220 (t80) REVERT: W 575 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6835 (mm-30) REVERT: W 588 ILE cc_start: 0.8443 (mt) cc_final: 0.8216 (mt) REVERT: W 600 LYS cc_start: 0.8585 (pttt) cc_final: 0.8343 (pttt) REVERT: W 613 VAL cc_start: 0.8510 (t) cc_final: 0.8192 (m) REVERT: W 628 LYS cc_start: 0.8562 (mttt) cc_final: 0.8094 (ttmm) REVERT: W 634 LYS cc_start: 0.7840 (mttt) cc_final: 0.7628 (mttt) REVERT: W 651 LYS cc_start: 0.7882 (tttm) cc_final: 0.7667 (mttm) REVERT: W 661 MET cc_start: 0.7358 (mmm) cc_final: 0.6976 (mmm) REVERT: W 691 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6978 (tm-30) REVERT: W 700 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8467 (mtmm) REVERT: W 703 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5449 (tp30) REVERT: W 717 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7618 (mm-30) REVERT: W 724 GLN cc_start: 0.7861 (tp40) cc_final: 0.7659 (tp40) REVERT: W 729 ILE cc_start: 0.7977 (mt) cc_final: 0.7581 (tt) REVERT: W 735 LYS cc_start: 0.7912 (mmtp) cc_final: 0.7442 (mmtp) REVERT: W 756 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7482 (mtpp) REVERT: W 757 LYS cc_start: 0.7889 (mttt) cc_final: 0.7160 (mmmm) REVERT: W 795 LYS cc_start: 0.8401 (mttt) cc_final: 0.8135 (mttt) REVERT: W 810 PHE cc_start: 0.7609 (m-80) cc_final: 0.7126 (m-80) REVERT: W 822 GLU cc_start: 0.7902 (tp30) cc_final: 0.7319 (tp30) REVERT: W 827 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7424 (mtm110) REVERT: W 828 GLN cc_start: 0.8012 (mp10) cc_final: 0.7555 (mp10) REVERT: W 832 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7371 (mm-40) REVERT: W 839 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7351 (mmtt) REVERT: W 869 LEU cc_start: 0.7290 (mp) cc_final: 0.7009 (tt) REVERT: W 877 ASP cc_start: 0.7435 (m-30) cc_final: 0.7078 (m-30) REVERT: W 885 ASP cc_start: 0.7693 (t0) cc_final: 0.7396 (m-30) REVERT: W 893 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7939 (tp-100) REVERT: W 903 GLN cc_start: 0.8415 (mm110) cc_final: 0.7792 (mm110) REVERT: W 909 ILE cc_start: 0.8071 (mp) cc_final: 0.7773 (mt) REVERT: W 919 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6932 (mt-10) REVERT: W 921 ASP cc_start: 0.7202 (t0) cc_final: 0.6810 (t0) REVERT: W 924 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7950 (mm-30) outliers start: 29 outliers final: 17 residues processed: 331 average time/residue: 0.1670 time to fit residues: 75.9582 Evaluate side-chains 336 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain W residue 278 MET Chi-restraints excluded: chain W residue 391 VAL 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 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 674 GLU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 722 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 = 0.3865 r_free = 0.3865 target = 0.149701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114394 restraints weight = 27077.808| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.54 r_work: 0.3230 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18996 Z= 0.200 Angle : 0.580 8.749 26995 Z= 0.337 Chirality : 0.038 0.185 3014 Planarity : 0.004 0.042 2320 Dihedral : 29.381 178.151 5044 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.89 % Allowed : 14.59 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.23), residues: 1395 helix: 2.20 (0.18), residues: 826 sheet: -0.02 (0.61), residues: 66 loop : -0.41 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 697 TYR 0.011 0.001 TYR F 51 PHE 0.011 0.001 PHE D 67 TRP 0.071 0.002 TRP W 491 HIS 0.004 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00451 (18993) covalent geometry : angle 0.57971 (26995) hydrogen bonds : bond 0.04461 ( 975) hydrogen bonds : angle 3.32014 ( 2506) Misc. bond : bond 0.00069 ( 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 343 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7724 (ttp80) REVERT: B 92 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7996 (mtp85) REVERT: C 77 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8234 (mtt180) REVERT: C 81 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7879 (tpt170) REVERT: D 31 LYS cc_start: 0.8289 (pptt) cc_final: 0.7907 (pptt) REVERT: F 85 ASP cc_start: 0.7816 (m-30) cc_final: 0.7560 (m-30) REVERT: W 302 ASP cc_start: 0.6538 (t0) cc_final: 0.4320 (m-30) REVERT: W 317 GLN cc_start: 0.5338 (mp10) cc_final: 0.5030 (mt0) REVERT: W 339 LYS cc_start: 0.8484 (mttt) cc_final: 0.8250 (mttt) REVERT: W 387 GLN cc_start: 0.8166 (mt0) cc_final: 0.7742 (mt0) REVERT: W 389 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7948 (mm-40) REVERT: W 416 LEU cc_start: 0.8081 (mt) cc_final: 0.7782 (mp) REVERT: W 432 LYS cc_start: 0.8070 (tppp) cc_final: 0.7795 (tppp) REVERT: W 433 PHE cc_start: 0.7948 (m-80) cc_final: 0.7682 (m-80) REVERT: W 437 ILE cc_start: 0.8478 (mp) cc_final: 0.8108 (tp) REVERT: W 481 LEU cc_start: 0.8531 (pp) cc_final: 0.8299 (pp) REVERT: W 485 GLN cc_start: 0.8144 (mt0) cc_final: 0.7763 (mt0) REVERT: W 498 LYS cc_start: 0.7751 (mttt) cc_final: 0.7513 (mttt) REVERT: W 526 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7204 (mt-10) REVERT: W 575 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6972 (mm-30) REVERT: W 588 ILE cc_start: 0.8438 (mt) cc_final: 0.8216 (mt) REVERT: W 600 LYS cc_start: 0.8594 (pttt) cc_final: 0.8341 (pttt) REVERT: W 611 ILE cc_start: 0.8332 (mt) cc_final: 0.7921 (pt) REVERT: W 613 VAL cc_start: 0.8464 (t) cc_final: 0.8142 (m) REVERT: W 628 LYS cc_start: 0.8529 (mttt) cc_final: 0.8100 (ttmm) REVERT: W 634 LYS cc_start: 0.7862 (mttt) cc_final: 0.7652 (mttt) REVERT: W 644 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6927 (m) REVERT: W 645 PRO cc_start: 0.7790 (Cg_endo) cc_final: 0.7561 (Cg_exo) REVERT: W 651 LYS cc_start: 0.7823 (tttm) cc_final: 0.7615 (mttm) REVERT: W 661 MET cc_start: 0.7325 (mmm) cc_final: 0.6955 (mmm) REVERT: W 691 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6958 (tm-30) REVERT: W 700 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8492 (mtmm) REVERT: W 703 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5582 (tp30) REVERT: W 724 GLN cc_start: 0.7921 (tp40) cc_final: 0.7694 (tp40) REVERT: W 729 ILE cc_start: 0.7964 (mt) cc_final: 0.7576 (tt) REVERT: W 735 LYS cc_start: 0.7933 (mmtp) cc_final: 0.7452 (mmtp) REVERT: W 756 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7480 (mtpp) REVERT: W 757 LYS cc_start: 0.7813 (mttt) cc_final: 0.7148 (mmmm) REVERT: W 795 LYS cc_start: 0.8408 (mttt) cc_final: 0.8158 (mttt) REVERT: W 810 PHE cc_start: 0.7582 (m-80) cc_final: 0.7160 (m-80) REVERT: W 822 GLU cc_start: 0.7903 (tp30) cc_final: 0.7357 (tp30) REVERT: W 827 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7405 (mtm110) REVERT: W 828 GLN cc_start: 0.7961 (mp10) cc_final: 0.7416 (mp10) REVERT: W 832 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7381 (mm-40) REVERT: W 839 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7351 (mmtt) REVERT: W 869 LEU cc_start: 0.7350 (mp) cc_final: 0.7072 (tt) REVERT: W 877 ASP cc_start: 0.7367 (m-30) cc_final: 0.7042 (m-30) REVERT: W 893 GLN cc_start: 0.8235 (tp-100) cc_final: 0.8019 (tp-100) REVERT: W 903 GLN cc_start: 0.8396 (mm110) cc_final: 0.8022 (tp-100) REVERT: W 919 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6894 (mt-10) REVERT: W 921 ASP cc_start: 0.7212 (t0) cc_final: 0.6781 (t0) REVERT: W 924 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7955 (mm-30) outliers start: 23 outliers final: 17 residues processed: 328 average time/residue: 0.1702 time to fit residues: 77.2442 Evaluate side-chains 343 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 322 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain W residue 278 MET 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 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 0.0470 chunk 31 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3864 r_free = 0.3864 target = 0.149647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114303 restraints weight = 27287.600| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.54 r_work: 0.3225 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18996 Z= 0.206 Angle : 0.587 10.106 26995 Z= 0.341 Chirality : 0.038 0.182 3014 Planarity : 0.004 0.046 2320 Dihedral : 29.330 177.164 5044 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.38 % Allowed : 15.25 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.23), residues: 1395 helix: 2.17 (0.18), residues: 826 sheet: 0.05 (0.61), residues: 60 loop : -0.37 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 40 TYR 0.012 0.001 TYR F 51 PHE 0.012 0.001 PHE D 67 TRP 0.079 0.002 TRP W 491 HIS 0.004 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00465 (18993) covalent geometry : angle 0.58696 (26995) hydrogen bonds : bond 0.04504 ( 975) hydrogen bonds : angle 3.34545 ( 2506) Misc. bond : bond 0.00070 ( 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 348 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 319 time to evaluate : 0.470 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: 0.8111 (ttp80) cc_final: 0.7715 (ttp80) REVERT: B 92 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7987 (mtp85) REVERT: C 77 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8236 (mtt180) REVERT: C 81 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7861 (tpt170) REVERT: D 31 LYS cc_start: 0.8287 (pptt) cc_final: 0.7910 (pptt) REVERT: F 85 ASP cc_start: 0.7777 (m-30) cc_final: 0.7516 (m-30) REVERT: W 302 ASP cc_start: 0.6594 (t0) cc_final: 0.4377 (m-30) REVERT: W 317 GLN cc_start: 0.5369 (mp10) cc_final: 0.5052 (mt0) REVERT: W 339 LYS cc_start: 0.8527 (mttt) cc_final: 0.8263 (mtmm) REVERT: W 387 GLN cc_start: 0.8178 (mt0) cc_final: 0.7755 (mt0) REVERT: W 389 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7797 (mm-40) REVERT: W 393 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7107 (ttt180) REVERT: W 416 LEU cc_start: 0.8087 (mt) cc_final: 0.7829 (mp) REVERT: W 432 LYS cc_start: 0.8102 (tppp) cc_final: 0.7784 (tppp) REVERT: W 433 PHE cc_start: 0.7963 (m-80) cc_final: 0.7691 (m-80) REVERT: W 437 ILE cc_start: 0.8510 (mp) cc_final: 0.8135 (tp) REVERT: W 492 LEU cc_start: 0.8370 (mt) cc_final: 0.8159 (mt) REVERT: W 498 LYS cc_start: 0.7745 (mttt) cc_final: 0.7507 (mttt) REVERT: W 507 GLU cc_start: 0.7983 (tt0) cc_final: 0.7674 (tt0) REVERT: W 575 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6583 (mm-30) REVERT: W 588 ILE cc_start: 0.8440 (mt) cc_final: 0.8217 (mt) REVERT: W 600 LYS cc_start: 0.8592 (pttt) cc_final: 0.8334 (pttt) REVERT: W 613 VAL cc_start: 0.8523 (t) cc_final: 0.8260 (m) REVERT: W 628 LYS cc_start: 0.8532 (mttt) cc_final: 0.8224 (ttmm) REVERT: W 644 THR cc_start: 0.7201 (OUTLIER) cc_final: 0.6953 (m) REVERT: W 645 PRO cc_start: 0.7815 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: W 651 LYS cc_start: 0.7807 (tttm) cc_final: 0.7570 (mttm) REVERT: W 661 MET cc_start: 0.7346 (mmm) cc_final: 0.6986 (mmm) REVERT: W 668 TRP cc_start: 0.8116 (t-100) cc_final: 0.7519 (t-100) REVERT: W 691 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7008 (tm-30) REVERT: W 700 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8491 (mtmm) REVERT: W 712 GLN cc_start: 0.7654 (pm20) cc_final: 0.7442 (pm20) REVERT: W 724 GLN cc_start: 0.7915 (tp40) cc_final: 0.7663 (tp40) REVERT: W 729 ILE cc_start: 0.7971 (mt) cc_final: 0.7592 (tt) REVERT: W 735 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7442 (mmtp) REVERT: W 756 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7476 (mtpp) REVERT: W 757 LYS cc_start: 0.7817 (mttt) cc_final: 0.7157 (mmmm) REVERT: W 795 LYS cc_start: 0.8400 (mttt) cc_final: 0.8167 (mttt) REVERT: W 810 PHE cc_start: 0.7582 (m-80) cc_final: 0.7136 (m-80) REVERT: W 822 GLU cc_start: 0.7876 (tp30) cc_final: 0.7296 (tp30) REVERT: W 828 GLN cc_start: 0.7874 (mp10) cc_final: 0.7370 (mp10) REVERT: W 832 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7399 (mm-40) REVERT: W 839 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7338 (mmtt) REVERT: W 877 ASP cc_start: 0.7371 (m-30) cc_final: 0.7054 (m-30) REVERT: W 885 ASP cc_start: 0.7648 (t0) cc_final: 0.7324 (m-30) REVERT: W 903 GLN cc_start: 0.8369 (mm110) cc_final: 0.7649 (mm-40) REVERT: W 919 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6888 (mt-10) REVERT: W 921 ASP cc_start: 0.7231 (t0) cc_final: 0.6775 (t0) REVERT: W 924 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7994 (mm-30) outliers start: 29 outliers final: 17 residues processed: 329 average time/residue: 0.1636 time to fit residues: 74.4882 Evaluate side-chains 338 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 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 584 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 119 optimal weight: 30.0000 chunk 157 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 121 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 893 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.113356 restraints weight = 27186.837| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.54 r_work: 0.3207 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 18996 Z= 0.246 Angle : 0.613 8.877 26995 Z= 0.353 Chirality : 0.040 0.188 3014 Planarity : 0.005 0.046 2320 Dihedral : 29.355 175.368 5044 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.13 % Allowed : 16.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.22), residues: 1395 helix: 2.08 (0.18), residues: 826 sheet: 0.07 (0.60), residues: 60 loop : -0.41 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 40 TYR 0.012 0.001 TYR W 410 PHE 0.013 0.001 PHE W 519 TRP 0.086 0.002 TRP W 491 HIS 0.004 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00556 (18993) covalent geometry : angle 0.61336 (26995) hydrogen bonds : bond 0.04742 ( 975) hydrogen bonds : angle 3.40724 ( 2506) Misc. bond : bond 0.00085 ( 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 330 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 0.434 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: 0.8118 (ttp80) cc_final: 0.7727 (ttp80) REVERT: B 92 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8045 (mtp85) REVERT: C 77 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (mtt180) REVERT: C 81 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7854 (tpt170) REVERT: D 31 LYS cc_start: 0.8277 (pptt) cc_final: 0.7905 (pptt) REVERT: D 43 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8327 (mmtt) REVERT: F 85 ASP cc_start: 0.7803 (m-30) cc_final: 0.7537 (m-30) REVERT: H 103 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7782 (mp) REVERT: W 302 ASP cc_start: 0.6762 (t0) cc_final: 0.4587 (m-30) REVERT: W 317 GLN cc_start: 0.5378 (mp10) cc_final: 0.5148 (mt0) REVERT: W 386 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7990 (mtmm) REVERT: W 387 GLN cc_start: 0.8239 (mt0) cc_final: 0.7814 (mt0) REVERT: W 389 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7931 (mm-40) REVERT: W 412 LYS cc_start: 0.7801 (tptp) cc_final: 0.7475 (tptt) REVERT: W 432 LYS cc_start: 0.8042 (tppp) cc_final: 0.7745 (tppp) REVERT: W 433 PHE cc_start: 0.7960 (m-80) cc_final: 0.7684 (m-80) REVERT: W 437 ILE cc_start: 0.8539 (mp) cc_final: 0.8154 (tp) REVERT: W 485 GLN cc_start: 0.8176 (mt0) cc_final: 0.7809 (mt0) REVERT: W 496 TRP cc_start: 0.8467 (t60) cc_final: 0.8136 (t-100) REVERT: W 498 LYS cc_start: 0.7779 (mttt) cc_final: 0.7541 (mttt) REVERT: W 507 GLU cc_start: 0.8010 (tt0) cc_final: 0.7717 (tt0) REVERT: W 526 GLU cc_start: 0.7306 (mp0) cc_final: 0.7102 (mp0) REVERT: W 545 TRP cc_start: 0.8544 (m100) cc_final: 0.8217 (m100) REVERT: W 575 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6957 (mm-30) REVERT: W 588 ILE cc_start: 0.8429 (mt) cc_final: 0.8188 (mt) REVERT: W 600 LYS cc_start: 0.8580 (pttt) cc_final: 0.8330 (pttt) REVERT: W 613 VAL cc_start: 0.8520 (t) cc_final: 0.8208 (m) REVERT: W 628 LYS cc_start: 0.8526 (mttt) cc_final: 0.8099 (ttmm) REVERT: W 644 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6969 (m) REVERT: W 651 LYS cc_start: 0.7836 (tttm) cc_final: 0.7592 (mttm) REVERT: W 661 MET cc_start: 0.7287 (mmm) cc_final: 0.6879 (mmm) REVERT: W 668 TRP cc_start: 0.8099 (t-100) cc_final: 0.7506 (t-100) REVERT: W 691 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7098 (tm-30) REVERT: W 700 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8335 (ptpp) REVERT: W 712 GLN cc_start: 0.7779 (pm20) cc_final: 0.7496 (pm20) REVERT: W 716 MET cc_start: 0.7388 (tpt) cc_final: 0.7180 (tpp) REVERT: W 717 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7725 (mm-30) REVERT: W 724 GLN cc_start: 0.7973 (tp40) cc_final: 0.7687 (tp40) REVERT: W 729 ILE cc_start: 0.7956 (mt) cc_final: 0.7596 (tt) REVERT: W 734 TYR cc_start: 0.7644 (m-80) cc_final: 0.7315 (m-80) REVERT: W 735 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7437 (mmtp) REVERT: W 756 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7488 (mtpp) REVERT: W 757 LYS cc_start: 0.7868 (mttt) cc_final: 0.7176 (mmmm) REVERT: W 795 LYS cc_start: 0.8449 (mttt) cc_final: 0.8244 (mttt) REVERT: W 810 PHE cc_start: 0.7590 (m-80) cc_final: 0.7138 (m-80) REVERT: W 822 GLU cc_start: 0.7883 (tp30) cc_final: 0.7207 (tp30) REVERT: W 826 TYR cc_start: 0.7332 (m-10) cc_final: 0.6663 (m-10) REVERT: W 832 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7413 (mm-40) REVERT: W 839 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7353 (mmtt) REVERT: W 877 ASP cc_start: 0.7406 (m-30) cc_final: 0.7076 (m-30) REVERT: W 903 GLN cc_start: 0.8355 (mm110) cc_final: 0.7629 (mm-40) REVERT: W 919 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6945 (mt-10) REVERT: W 921 ASP cc_start: 0.7267 (t0) cc_final: 0.6813 (t0) REVERT: W 924 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8017 (mm-30) outliers start: 26 outliers final: 18 residues processed: 315 average time/residue: 0.1753 time to fit residues: 76.1887 Evaluate side-chains 321 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 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 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 650 LEU Chi-restraints excluded: chain W residue 711 GLU Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN W 327 HIS W 329 HIS ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116230 restraints weight = 27268.970| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.54 r_work: 0.3254 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3633 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= 0.164 Angle : 0.572 9.035 26995 Z= 0.331 Chirality : 0.036 0.192 3014 Planarity : 0.004 0.041 2320 Dihedral : 29.266 178.736 5044 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.48 % Allowed : 16.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.23), residues: 1395 helix: 2.27 (0.18), residues: 833 sheet: 0.13 (0.59), residues: 60 loop : -0.36 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 40 TYR 0.012 0.001 TYR D 80 PHE 0.019 0.001 PHE W 519 TRP 0.071 0.002 TRP W 491 HIS 0.004 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00363 (18993) covalent geometry : angle 0.57175 (26995) hydrogen bonds : bond 0.04211 ( 975) hydrogen bonds : angle 3.25488 ( 2506) Misc. bond : bond 0.00065 ( 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 325 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7721 (ttp80) REVERT: B 92 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: C 65 LEU cc_start: 0.8603 (mt) cc_final: 0.8260 (mp) REVERT: C 77 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8225 (mtt180) REVERT: C 81 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7893 (tpt170) REVERT: D 31 LYS cc_start: 0.8306 (pptt) cc_final: 0.7920 (pptt) REVERT: D 56 MET cc_start: 0.8119 (mmm) cc_final: 0.7866 (tmm) REVERT: F 84 MET cc_start: 0.8211 (mmm) cc_final: 0.7843 (mmm) REVERT: H 56 MET cc_start: 0.8343 (tpp) cc_final: 0.7461 (tpp) REVERT: H 103 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7729 (mp) REVERT: W 302 ASP cc_start: 0.6672 (t0) cc_final: 0.4548 (m-30) REVERT: W 386 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8130 (mtmm) REVERT: W 387 GLN cc_start: 0.8207 (mt0) cc_final: 0.7868 (mt0) REVERT: W 393 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7020 (ttp-170) REVERT: W 412 LYS cc_start: 0.7896 (tptp) cc_final: 0.7530 (tptt) REVERT: W 432 LYS cc_start: 0.8024 (tppp) cc_final: 0.7709 (tppp) REVERT: W 433 PHE cc_start: 0.7940 (m-80) cc_final: 0.7673 (m-10) REVERT: W 437 ILE cc_start: 0.8491 (mp) cc_final: 0.8105 (tp) REVERT: W 485 GLN cc_start: 0.8078 (mt0) cc_final: 0.7741 (mt0) REVERT: W 496 TRP cc_start: 0.8406 (t60) cc_final: 0.8162 (t-100) REVERT: W 498 LYS cc_start: 0.7716 (mttt) cc_final: 0.7446 (mttt) REVERT: W 507 GLU cc_start: 0.7836 (tt0) cc_final: 0.7611 (tt0) REVERT: W 512 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7433 (mtmm) REVERT: W 545 TRP cc_start: 0.8520 (m100) cc_final: 0.8129 (m100) REVERT: W 560 VAL cc_start: 0.8864 (m) cc_final: 0.8554 (p) REVERT: W 588 ILE cc_start: 0.8392 (mt) cc_final: 0.8163 (mt) REVERT: W 600 LYS cc_start: 0.8559 (pttt) cc_final: 0.8287 (pttt) REVERT: W 613 VAL cc_start: 0.8476 (t) cc_final: 0.8175 (m) REVERT: W 628 LYS cc_start: 0.8525 (mttt) cc_final: 0.8123 (ttmm) REVERT: W 644 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6900 (m) REVERT: W 661 MET cc_start: 0.7323 (mmm) cc_final: 0.6922 (mmm) REVERT: W 668 TRP cc_start: 0.8063 (t-100) cc_final: 0.7547 (t-100) REVERT: W 691 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7024 (tm-30) REVERT: W 700 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8510 (mtmm) REVERT: W 712 GLN cc_start: 0.7696 (pm20) cc_final: 0.7282 (pm20) REVERT: W 717 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7717 (mm-30) REVERT: W 724 GLN cc_start: 0.7921 (tp40) cc_final: 0.7602 (tp40) REVERT: W 729 ILE cc_start: 0.7919 (mt) cc_final: 0.7580 (tt) REVERT: W 734 TYR cc_start: 0.7634 (m-80) cc_final: 0.7319 (m-80) REVERT: W 735 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7414 (mmtp) REVERT: W 756 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7457 (mtpp) REVERT: W 757 LYS cc_start: 0.7749 (mttt) cc_final: 0.7134 (mmmm) REVERT: W 795 LYS cc_start: 0.8470 (mttt) cc_final: 0.8265 (mttt) REVERT: W 803 ARG cc_start: 0.7904 (mmp80) cc_final: 0.7634 (mmp80) REVERT: W 810 PHE cc_start: 0.7585 (m-80) cc_final: 0.7137 (m-80) REVERT: W 812 GLN cc_start: 0.6975 (pt0) cc_final: 0.6728 (pt0) REVERT: W 822 GLU cc_start: 0.7859 (tp30) cc_final: 0.7166 (tp30) REVERT: W 826 TYR cc_start: 0.7315 (m-10) cc_final: 0.6592 (m-10) REVERT: W 832 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7314 (mm-40) REVERT: W 839 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7387 (mmmt) REVERT: W 877 ASP cc_start: 0.7354 (m-30) cc_final: 0.7026 (m-30) REVERT: W 903 GLN cc_start: 0.8318 (mm110) cc_final: 0.7689 (mm110) REVERT: W 919 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6919 (mt-10) REVERT: W 921 ASP cc_start: 0.7211 (t0) cc_final: 0.6736 (t0) REVERT: W 924 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 18 outliers final: 13 residues processed: 316 average time/residue: 0.1776 time to fit residues: 77.5417 Evaluate side-chains 319 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 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 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 101 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: B 64 ASN ** W 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115414 restraints weight = 27090.490| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.54 r_work: 0.3223 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3736 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= 0.186 Angle : 0.586 8.916 26995 Z= 0.336 Chirality : 0.037 0.192 3014 Planarity : 0.004 0.055 2320 Dihedral : 29.221 177.775 5044 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.39 % Allowed : 17.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1395 helix: 2.26 (0.18), residues: 833 sheet: 0.12 (0.60), residues: 60 loop : -0.37 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 583 TYR 0.013 0.001 TYR D 80 PHE 0.017 0.001 PHE W 519 TRP 0.076 0.002 TRP W 491 HIS 0.005 0.001 HIS W 385 Details of bonding type rmsd covalent geometry : bond 0.00417 (18993) covalent geometry : angle 0.58590 (26995) hydrogen bonds : bond 0.04329 ( 975) hydrogen bonds : angle 3.27420 ( 2506) Misc. bond : bond 0.00068 ( 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 318 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 301 time to evaluate : 0.445 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: 0.8097 (ttp80) cc_final: 0.7690 (ttp80) REVERT: B 92 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7955 (mtp85) REVERT: C 65 LEU cc_start: 0.8568 (mt) cc_final: 0.8345 (mp) REVERT: C 77 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8239 (mtt180) REVERT: C 81 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7864 (tpt170) REVERT: D 31 LYS cc_start: 0.8296 (pptt) cc_final: 0.7920 (pptt) REVERT: H 56 MET cc_start: 0.8364 (tpp) cc_final: 0.7461 (tpp) REVERT: W 302 ASP cc_start: 0.6771 (t0) cc_final: 0.4614 (m-30) REVERT: W 386 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8108 (mtmm) REVERT: W 387 GLN cc_start: 0.8254 (mt0) cc_final: 0.7864 (mt0) REVERT: W 393 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7429 (ttt180) REVERT: W 412 LYS cc_start: 0.7885 (tptp) cc_final: 0.7530 (tptt) REVERT: W 432 LYS cc_start: 0.8053 (tppp) cc_final: 0.7748 (tppp) REVERT: W 433 PHE cc_start: 0.7965 (m-80) cc_final: 0.7684 (m-10) REVERT: W 437 ILE cc_start: 0.8559 (mp) cc_final: 0.8163 (tp) REVERT: W 485 GLN cc_start: 0.8095 (mt0) cc_final: 0.7729 (mt0) REVERT: W 498 LYS cc_start: 0.7737 (mttt) cc_final: 0.7474 (mttt) REVERT: W 512 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7484 (mtmm) REVERT: W 560 VAL cc_start: 0.8864 (m) cc_final: 0.8543 (p) REVERT: W 588 ILE cc_start: 0.8384 (mt) cc_final: 0.8149 (mt) REVERT: W 600 LYS cc_start: 0.8572 (pttt) cc_final: 0.8299 (pttt) REVERT: W 613 VAL cc_start: 0.8483 (t) cc_final: 0.8155 (m) REVERT: W 628 LYS cc_start: 0.8517 (mttt) cc_final: 0.8110 (ttmm) REVERT: W 644 THR cc_start: 0.7116 (OUTLIER) cc_final: 0.6887 (m) REVERT: W 661 MET cc_start: 0.7312 (mmm) cc_final: 0.6926 (mmm) REVERT: W 664 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7781 (mmmt) REVERT: W 668 TRP cc_start: 0.7965 (t-100) cc_final: 0.7677 (t-100) REVERT: W 691 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7108 (tm-30) REVERT: W 700 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8576 (mtmm) REVERT: W 712 GLN cc_start: 0.7726 (pm20) cc_final: 0.7504 (pm20) REVERT: W 716 MET cc_start: 0.7527 (tpp) cc_final: 0.7147 (tpp) REVERT: W 717 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7659 (mm-30) REVERT: W 724 GLN cc_start: 0.7937 (tp40) cc_final: 0.7626 (tp40) REVERT: W 729 ILE cc_start: 0.7908 (mt) cc_final: 0.7552 (tt) REVERT: W 734 TYR cc_start: 0.7645 (m-80) cc_final: 0.7322 (m-80) REVERT: W 735 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7402 (mmtp) REVERT: W 756 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7435 (mtpp) REVERT: W 757 LYS cc_start: 0.7821 (mttt) cc_final: 0.7169 (mmmm) REVERT: W 789 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8106 (tppt) REVERT: W 810 PHE cc_start: 0.7580 (m-80) cc_final: 0.7131 (m-80) REVERT: W 812 GLN cc_start: 0.6971 (pt0) cc_final: 0.6720 (pt0) REVERT: W 822 GLU cc_start: 0.7847 (tp30) cc_final: 0.7254 (tp30) REVERT: W 832 GLN cc_start: 0.7581 (mm110) cc_final: 0.7291 (mm110) REVERT: W 839 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7395 (mmmt) REVERT: W 877 ASP cc_start: 0.7359 (m-30) cc_final: 0.7037 (m-30) REVERT: W 893 GLN cc_start: 0.8364 (tp40) cc_final: 0.7784 (tp40) REVERT: W 903 GLN cc_start: 0.8377 (mm110) cc_final: 0.7701 (tp40) REVERT: W 919 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6898 (mt-10) REVERT: W 921 ASP cc_start: 0.7205 (t0) cc_final: 0.6728 (t0) REVERT: W 924 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7977 (mm-30) outliers start: 17 outliers final: 13 residues processed: 309 average time/residue: 0.1736 time to fit residues: 73.7603 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 : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain 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 639 LEU Chi-restraints excluded: chain W residue 642 THR Chi-restraints excluded: chain W residue 644 THR Chi-restraints excluded: chain W residue 651 LYS Chi-restraints excluded: chain W residue 892 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114894 restraints weight = 27313.598| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.55 r_work: 0.3233 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18996 Z= 0.200 Angle : 0.588 8.761 26995 Z= 0.338 Chirality : 0.038 0.193 3014 Planarity : 0.004 0.044 2320 Dihedral : 29.214 177.736 5044 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.72 % Allowed : 16.89 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.23), residues: 1395 helix: 2.23 (0.18), residues: 833 sheet: 0.23 (0.61), residues: 60 loop : -0.40 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG W 583 TYR 0.014 0.001 TYR D 80 PHE 0.015 0.001 PHE W 519 TRP 0.066 0.002 TRP W 491 HIS 0.005 0.001 HIS W 849 Details of bonding type rmsd covalent geometry : bond 0.00451 (18993) covalent geometry : angle 0.58804 (26995) hydrogen bonds : bond 0.04404 ( 975) hydrogen bonds : angle 3.29663 ( 2506) Misc. bond : bond 0.00075 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.82 seconds wall clock time: 88 minutes 40.13 seconds (5320.13 seconds total)