Starting phenix.real_space_refine on Mon Jun 16 02:58:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.map" model { file = "/net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nh8_49406/06_2025/9nh8_49406.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 312 5.49 5 S 38 5.16 5 C 10690 2.51 5 N 3398 2.21 5 O 4062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18500 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} 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: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3178 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3218 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} 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: "W" Number of atoms: 6021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 6021 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 22, 'TRANS': 705} Chain breaks: 4 Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Time building chain proxies: 11.63, per 1000 atoms: 0.63 Number of scatterers: 18500 At special positions: 0 Unit cell: (109.56, 151.06, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 312 15.00 O 4062 8.00 N 3398 7.00 C 10690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2806 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 14 sheets defined 62.8% alpha, 4.2% beta 105 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.736A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.590A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.566A 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 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.648A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.511A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.735A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 77 removed outlier: 3.722A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.241A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.770A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.834A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.654A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.805A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.721A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.558A pdb=" N TYR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'W' and resid 293 through 301 Processing helix chain 'W' and resid 335 through 341 removed outlier: 4.072A pdb=" N LYS W 339 " --> pdb=" O GLU W 335 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 364 removed outlier: 3.681A pdb=" N ASP W 350 " --> pdb=" O MET W 346 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG W 361 " --> pdb=" O GLN W 357 " (cutoff:3.500A) Processing helix chain 'W' and resid 367 through 388 removed outlier: 3.506A pdb=" N ASP W 383 " --> pdb=" O GLU W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 409 Processing helix chain 'W' and resid 417 through 421 Processing helix chain 'W' and resid 428 through 433 Processing helix chain 'W' and resid 433 through 446 removed outlier: 4.105A pdb=" N GLU W 439 " --> pdb=" O ALA W 435 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN W 444 " --> pdb=" O TYR W 440 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN W 445 " --> pdb=" O PHE W 441 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER W 446 " --> pdb=" O SER W 442 " (cutoff:3.500A) Processing helix chain 'W' and resid 470 through 474 Processing helix chain 'W' and resid 482 through 498 Processing helix chain 'W' and resid 509 through 512 removed outlier: 3.689A pdb=" N LYS W 512 " --> pdb=" O GLY W 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 509 through 512' Processing helix chain 'W' and resid 513 through 520 removed outlier: 3.750A pdb=" N LEU W 520 " --> pdb=" O THR W 516 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 552 removed outlier: 4.640A pdb=" N THR W 543 " --> pdb=" O LEU W 539 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER W 544 " --> pdb=" O SER W 540 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN W 550 " --> pdb=" O GLN W 546 " (cutoff:3.500A) Processing helix chain 'W' and resid 564 through 575 Processing helix chain 'W' and resid 592 through 599 removed outlier: 3.615A pdb=" N LEU W 597 " --> pdb=" O TYR W 593 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS W 598 " --> pdb=" O GLU W 594 " (cutoff:3.500A) Processing helix chain 'W' and resid 599 through 605 Processing helix chain 'W' and resid 615 through 620 removed outlier: 3.783A pdb=" N ARG W 618 " --> pdb=" O GLU W 615 " (cutoff:3.500A) Processing helix chain 'W' and resid 624 through 632 removed outlier: 3.787A pdb=" N ASP W 632 " --> pdb=" O LYS W 628 " (cutoff:3.500A) Processing helix chain 'W' and resid 649 through 661 removed outlier: 3.609A pdb=" N LEU W 653 " --> pdb=" O SER W 649 " (cutoff:3.500A) Processing helix chain 'W' and resid 671 through 676 Processing helix chain 'W' and resid 680 through 685 Processing helix chain 'W' and resid 698 through 703 removed outlier: 3.694A pdb=" N VAL W 702 " --> pdb=" O VAL W 698 " (cutoff:3.500A) Processing helix chain 'W' and resid 719 through 733 Processing helix chain 'W' and resid 733 through 738 Processing helix chain 'W' and resid 739 through 743 Processing helix chain 'W' and resid 744 through 760 removed outlier: 3.647A pdb=" N LYS W 757 " --> pdb=" O MET W 753 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS W 758 " --> pdb=" O GLU W 754 " (cutoff:3.500A) Processing helix chain 'W' and resid 761 through 765 removed outlier: 3.504A pdb=" N LEU W 764 " --> pdb=" O HIS W 761 " (cutoff:3.500A) Processing helix chain 'W' and resid 769 through 774 Processing helix chain 'W' and resid 775 through 787 removed outlier: 3.814A pdb=" N LEU W 780 " --> pdb=" O LYS W 776 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN W 781 " --> pdb=" O GLN W 777 " (cutoff:3.500A) Processing helix chain 'W' and resid 790 through 804 removed outlier: 4.328A pdb=" N LYS W 795 " --> pdb=" O ILE W 791 " (cutoff:3.500A) Processing helix chain 'W' and resid 813 through 828 Processing helix chain 'W' and resid 839 through 852 Processing helix chain 'W' and resid 863 through 870 removed outlier: 3.688A pdb=" N GLY W 868 " --> pdb=" O ARG W 865 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY W 870 " --> pdb=" O GLY W 867 " (cutoff:3.500A) Processing helix chain 'W' and resid 887 through 897 removed outlier: 3.847A pdb=" N ASP W 891 " --> pdb=" O ASN W 887 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG W 897 " --> pdb=" O GLN W 893 " (cutoff:3.500A) Processing helix chain 'W' and resid 919 through 927 removed outlier: 4.226A pdb=" N ARG W 925 " --> pdb=" O ASP W 921 " (cutoff:3.500A) Processing helix chain 'W' and resid 961 through 972 removed outlier: 3.519A pdb=" N LEU W 969 " --> pdb=" O LEU W 965 " (cutoff:3.500A) Processing helix chain 'W' and resid 994 through 999 Processing helix chain 'W' and resid 1042 through 1047 Processing helix chain 'W' and resid 1049 through 1069 removed outlier: 3.705A pdb=" N ARG W1053 " --> pdb=" O GLU W1049 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU W1058 " --> pdb=" O ARG W1054 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN W1061 " --> pdb=" O GLU W1057 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU W1064 " --> pdb=" O ARG W1060 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE W1067 " --> pdb=" O GLU W1063 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A 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: 7.120A 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: 6.971A 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: 6.705A 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: 7.254A 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 274 through 276 Processing sheet with id=AB3, first strand: chain 'W' and resid 391 through 394 removed outlier: 4.045A pdb=" N ARG W 393 " --> pdb=" O LYS W 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 502 through 504 removed outlier: 3.586A pdb=" N CYS W 502 " --> pdb=" O ARG W 638 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE W 611 " --> pdb=" O LEU W 639 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE W 641 " --> pdb=" O ILE W 611 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL W 613 " --> pdb=" O ILE W 641 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'W' and resid 712 through 715 removed outlier: 3.877A pdb=" N GLN W 712 " --> pdb=" O ILE W 909 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU W 808 " --> pdb=" O VAL W 880 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL W 807 " --> pdb=" O PHE W 860 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU W 862 " --> pdb=" O VAL W 807 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE W 809 " --> pdb=" O LEU W 862 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN W 832 " --> pdb=" O LEU W 861 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 105 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 9.83 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2452 1.32 - 1.44: 6717 1.44 - 1.57: 9629 1.57 - 1.70: 624 1.70 - 1.82: 63 Bond restraints: 19485 Sorted by residual: bond pdb=" CB ML3 V 4 " pdb=" SG ML3 V 4 " ideal model delta sigma weight residual 1.817 1.511 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" SG ML3 V 4 " pdb=" CD ML3 V 4 " ideal model delta sigma weight residual 1.815 1.520 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C PRO C 80 " pdb=" O PRO C 80 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.16e-02 7.43e+03 1.44e+01 bond pdb=" CA GLN W 340 " pdb=" C GLN W 340 " ideal model delta sigma weight residual 1.522 1.566 -0.044 1.38e-02 5.25e+03 1.01e+01 bond pdb=" N LEU W 319 " pdb=" CA LEU W 319 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.41e-02 5.03e+03 9.33e+00 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 27188 2.37 - 4.74: 374 4.74 - 7.12: 39 7.12 - 9.49: 13 9.49 - 11.86: 5 Bond angle restraints: 27619 Sorted by residual: angle pdb=" N ILE W 320 " pdb=" CA ILE W 320 " pdb=" C ILE W 320 " ideal model delta sigma weight residual 108.85 116.63 -7.78 1.54e+00 4.22e-01 2.55e+01 angle pdb=" CA PRO W 461 " pdb=" N PRO W 461 " pdb=" CD PRO W 461 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" N TYR W 593 " pdb=" CA TYR W 593 " pdb=" C TYR W 593 " ideal model delta sigma weight residual 112.54 106.75 5.79 1.22e+00 6.72e-01 2.25e+01 angle pdb=" N THR B 30 " pdb=" CA THR B 30 " pdb=" C THR B 30 " ideal model delta sigma weight residual 110.35 116.62 -6.27 1.38e+00 5.25e-01 2.06e+01 angle pdb=" CA GLN W 341 " pdb=" CB GLN W 341 " pdb=" CG GLN W 341 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 27614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 9326 34.86 - 69.73: 1569 69.73 - 104.59: 39 104.59 - 139.45: 0 139.45 - 174.31: 3 Dihedral angle restraints: 10937 sinusoidal: 6594 harmonic: 4343 Sorted by residual: dihedral pdb=" CA HIS W 476 " pdb=" C HIS W 476 " pdb=" N GLU W 477 " pdb=" CA GLU W 477 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLY W 405 " pdb=" C GLY W 405 " pdb=" N TYR W 406 " pdb=" CA TYR W 406 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA TYR W 406 " pdb=" C TYR W 406 " pdb=" N PRO W 407 " pdb=" CA PRO W 407 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 10934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2844 0.078 - 0.157: 212 0.157 - 0.235: 5 0.235 - 0.313: 3 0.313 - 0.391: 3 Chirality restraints: 3067 Sorted by residual: 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 -2.74 -0.39 2.00e-01 2.50e+01 3.83e+00 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 -2.72 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" P DA J -72 " pdb=" OP1 DA J -72 " pdb=" OP2 DA J -72 " pdb=" O5' DA J -72 " both_signs ideal model delta sigma weight residual True 2.35 -2.69 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 3064 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 28 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C GLY B 28 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY B 28 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE B 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.038 2.00e-02 2.50e+03 1.74e-02 8.33e+00 pdb=" N9 DA I 17 " 0.040 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -18 " -0.030 2.00e-02 2.50e+03 1.79e-02 7.21e+00 pdb=" N1 DC I -18 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DC I -18 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I -18 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC I -18 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC I -18 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC I -18 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC I -18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I -18 " 0.010 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 250 2.64 - 3.20: 15911 3.20 - 3.77: 30687 3.77 - 4.33: 41765 4.33 - 4.90: 61505 Nonbonded interactions: 150118 Sorted by model distance: nonbonded pdb=" O GLN W 341 " pdb=" NE2 GLN W 341 " model vdw 2.074 3.120 nonbonded pdb=" OD1 ASN W 648 " pdb=" N SER W 649 " model vdw 2.119 3.120 nonbonded pdb=" O LEU W 597 " pdb=" NZ LYS W 600 " model vdw 2.197 3.120 nonbonded pdb=" OD2 ASP F 68 " pdb=" NH1 ARG F 92 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG B 78 " pdb=" OD2 ASP B 85 " model vdw 2.208 3.120 ... (remaining 150113 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' and resid 14 through 118) selection = (chain 'G' and resid 14 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: 2.770 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: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 49.150 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.005 0.306 19485 Z= 0.261 Angle : 0.764 11.861 27619 Z= 0.438 Chirality : 0.044 0.391 3067 Planarity : 0.005 0.057 2430 Dihedral : 25.583 174.314 8131 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 0.78 % Allowed : 12.01 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1462 helix: -0.09 (0.17), residues: 830 sheet: -0.61 (0.79), residues: 53 loop : -0.94 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP W 413 HIS 0.027 0.002 HIS W 476 PHE 0.019 0.002 PHE W 882 TYR 0.023 0.002 TYR B 98 ARG 0.011 0.001 ARG W 443 Details of bonding type rmsd hydrogen bonds : bond 0.18513 ( 902) hydrogen bonds : angle 6.19756 ( 2362) covalent geometry : bond 0.00534 (19485) covalent geometry : angle 0.76398 (27619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 241 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 VAL cc_start: 0.7969 (t) cc_final: 0.7763 (p) REVERT: E 87 SER cc_start: 0.8445 (p) cc_final: 0.8175 (t) REVERT: F 80 THR cc_start: 0.8329 (m) cc_final: 0.7901 (m) REVERT: G 97 LEU cc_start: 0.7675 (mt) cc_final: 0.7373 (mt) REVERT: H 56 MET cc_start: 0.7739 (mmm) cc_final: 0.7416 (tpp) REVERT: W 317 GLN cc_start: 0.4611 (mm-40) cc_final: 0.4284 (tp40) REVERT: W 320 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6648 (mp) REVERT: W 323 LYS cc_start: 0.6722 (tttt) cc_final: 0.6251 (ptmt) REVERT: W 341 GLN cc_start: 0.6821 (tp40) cc_final: 0.6292 (mm-40) REVERT: W 537 VAL cc_start: 0.8079 (m) cc_final: 0.7812 (p) REVERT: W 570 MET cc_start: 0.7456 (tpp) cc_final: 0.7016 (mpp) REVERT: W 629 THR cc_start: 0.8118 (t) cc_final: 0.7734 (m) REVERT: W 652 GLU cc_start: 0.7348 (tt0) cc_final: 0.6956 (tt0) REVERT: W 661 MET cc_start: 0.7098 (mtt) cc_final: 0.6683 (mtt) REVERT: W 693 PHE cc_start: 0.6037 (m-80) cc_final: 0.5557 (m-80) REVERT: W 1069 MET cc_start: 0.5173 (mmm) cc_final: 0.4794 (mmm) outliers start: 10 outliers final: 7 residues processed: 246 average time/residue: 0.4175 time to fit residues: 146.8667 Evaluate side-chains 226 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain W residue 319 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 360 LYS Chi-restraints excluded: chain W residue 385 HIS Chi-restraints excluded: chain W residue 395 ILE Chi-restraints excluded: chain W residue 547 ARG Chi-restraints excluded: chain W residue 579 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 40.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 24 GLN H 44 GLN W 445 GLN W 521 ASN W 587 ASN W 636 ASN W 637 HIS W 658 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.178248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135086 restraints weight = 27789.763| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.75 r_work: 0.3499 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19485 Z= 0.253 Angle : 0.698 8.540 27619 Z= 0.401 Chirality : 0.044 0.327 3067 Planarity : 0.005 0.046 2430 Dihedral : 28.855 178.685 5081 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 12.25 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1462 helix: 0.56 (0.18), residues: 841 sheet: -0.59 (0.72), residues: 61 loop : -1.21 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP W 491 HIS 0.011 0.002 HIS W 476 PHE 0.019 0.002 PHE W 748 TYR 0.022 0.002 TYR W 388 ARG 0.007 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.05324 ( 902) hydrogen bonds : angle 4.03051 ( 2362) covalent geometry : bond 0.00567 (19485) covalent geometry : angle 0.69835 (27619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7932 (mmm) cc_final: 0.7648 (tpp) REVERT: C 29 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6671 (ttp-170) REVERT: C 95 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8322 (ttmm) REVERT: E 77 ASP cc_start: 0.8288 (t0) cc_final: 0.8077 (t0) REVERT: E 90 MET cc_start: 0.7309 (tpp) cc_final: 0.6875 (mpp) REVERT: F 84 MET cc_start: 0.7333 (mmm) cc_final: 0.7005 (mmm) REVERT: G 36 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8252 (mmmm) REVERT: G 74 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8292 (mtpp) REVERT: H 56 MET cc_start: 0.7990 (mmm) cc_final: 0.7619 (mmm) REVERT: W 276 ARG cc_start: 0.6388 (ttt180) cc_final: 0.5707 (ttt90) REVERT: W 278 MET cc_start: 0.4405 (mmm) cc_final: 0.4122 (mmm) REVERT: W 317 GLN cc_start: 0.5404 (mm-40) cc_final: 0.4906 (mm-40) REVERT: W 318 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5834 (p90) REVERT: W 319 LEU cc_start: 0.2579 (OUTLIER) cc_final: 0.2296 (mt) REVERT: W 323 LYS cc_start: 0.7086 (tttt) cc_final: 0.6688 (ttpt) REVERT: W 353 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8041 (mtmm) REVERT: W 412 LYS cc_start: 0.6857 (tttm) cc_final: 0.6642 (ttmt) REVERT: W 507 GLU cc_start: 0.6930 (tt0) cc_final: 0.6283 (tt0) REVERT: W 568 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7779 (mtm-85) REVERT: W 570 MET cc_start: 0.7483 (tpp) cc_final: 0.7077 (mpp) REVERT: W 615 GLU cc_start: 0.7804 (mp0) cc_final: 0.7473 (mp0) REVERT: W 627 TYR cc_start: 0.8289 (t80) cc_final: 0.7460 (t80) REVERT: W 629 THR cc_start: 0.8242 (t) cc_final: 0.7915 (m) REVERT: W 816 MET cc_start: 0.7656 (tpt) cc_final: 0.7153 (tpt) REVERT: W 920 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6248 (tm-30) REVERT: W 1050 ASP cc_start: 0.7217 (p0) cc_final: 0.6550 (t0) REVERT: W 1059 GLU cc_start: 0.6985 (tp30) cc_final: 0.6505 (tp30) REVERT: W 1062 LYS cc_start: 0.6386 (ttpt) cc_final: 0.6176 (ttpt) REVERT: W 1069 MET cc_start: 0.6562 (mmm) cc_final: 0.6356 (mmm) outliers start: 31 outliers final: 14 residues processed: 220 average time/residue: 0.4819 time to fit residues: 149.4634 Evaluate side-chains 200 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 318 TYR Chi-restraints excluded: chain W residue 319 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 573 THR Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 695 LEU Chi-restraints excluded: chain W residue 728 TRP Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN G 73 ASN W 327 HIS W 515 GLN W 579 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.175770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132690 restraints weight = 27487.600| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.73 r_work: 0.3463 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19485 Z= 0.202 Angle : 0.589 8.030 27619 Z= 0.345 Chirality : 0.039 0.244 3067 Planarity : 0.004 0.042 2430 Dihedral : 28.805 177.753 5064 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.11 % Allowed : 14.27 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1462 helix: 1.16 (0.18), residues: 834 sheet: -0.52 (0.73), residues: 61 loop : -0.92 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP W 491 HIS 0.007 0.001 HIS W 675 PHE 0.043 0.002 PHE W 748 TYR 0.016 0.001 TYR F 98 ARG 0.005 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 902) hydrogen bonds : angle 3.69291 ( 2362) covalent geometry : bond 0.00455 (19485) covalent geometry : angle 0.58920 (27619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6948 (ttp-170) REVERT: C 95 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8462 (ttmm) REVERT: E 77 ASP cc_start: 0.8306 (t0) cc_final: 0.8016 (t0) REVERT: E 90 MET cc_start: 0.7358 (tpp) cc_final: 0.6985 (mpp) REVERT: F 84 MET cc_start: 0.7400 (mmm) cc_final: 0.7040 (mmm) REVERT: G 36 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8391 (mtpp) REVERT: G 74 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8337 (mtpp) REVERT: W 276 ARG cc_start: 0.6389 (ttt180) cc_final: 0.5589 (ttt90) REVERT: W 278 MET cc_start: 0.4659 (mmm) cc_final: 0.4335 (mmm) REVERT: W 319 LEU cc_start: 0.2410 (OUTLIER) cc_final: 0.1949 (mt) REVERT: W 320 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6853 (mt) REVERT: W 323 LYS cc_start: 0.7343 (tttt) cc_final: 0.6919 (ptmt) REVERT: W 393 ARG cc_start: 0.7545 (ptp90) cc_final: 0.7312 (ttp-110) REVERT: W 412 LYS cc_start: 0.6845 (tttm) cc_final: 0.6476 (ttpt) REVERT: W 445 GLN cc_start: 0.8001 (mp10) cc_final: 0.7673 (pm20) REVERT: W 503 ILE cc_start: 0.8322 (mp) cc_final: 0.8111 (mm) REVERT: W 507 GLU cc_start: 0.7029 (tt0) cc_final: 0.6252 (tt0) REVERT: W 565 ILE cc_start: 0.7277 (mm) cc_final: 0.7024 (mp) REVERT: W 568 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7489 (mtm-85) REVERT: W 570 MET cc_start: 0.7446 (tpp) cc_final: 0.7046 (mpp) REVERT: W 629 THR cc_start: 0.8290 (t) cc_final: 0.8000 (m) REVERT: W 652 GLU cc_start: 0.7509 (tt0) cc_final: 0.7157 (pt0) REVERT: W 690 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7641 (pp) REVERT: W 757 LYS cc_start: 0.8100 (mttt) cc_final: 0.7592 (mttt) REVERT: W 1069 MET cc_start: 0.6973 (mmm) cc_final: 0.6584 (mmm) outliers start: 27 outliers final: 12 residues processed: 209 average time/residue: 0.4038 time to fit residues: 119.1762 Evaluate side-chains 203 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 319 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 690 LEU Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 149 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN W 341 GLN W 378 GLN W 434 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.176072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133454 restraints weight = 27828.304| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.70 r_work: 0.3494 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19485 Z= 0.158 Angle : 0.545 8.184 27619 Z= 0.320 Chirality : 0.036 0.145 3067 Planarity : 0.004 0.041 2430 Dihedral : 28.580 173.911 5064 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.42 % Allowed : 14.43 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1462 helix: 1.54 (0.18), residues: 840 sheet: -0.07 (0.77), residues: 56 loop : -0.94 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.030 0.001 PHE W 748 TYR 0.018 0.001 TYR W 374 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 902) hydrogen bonds : angle 3.41681 ( 2362) covalent geometry : bond 0.00347 (19485) covalent geometry : angle 0.54498 (27619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7461 (mmm) REVERT: C 29 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6869 (ttp-170) REVERT: C 72 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: C 95 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8261 (ttmm) REVERT: D 90 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: E 77 ASP cc_start: 0.8302 (t0) cc_final: 0.7995 (t0) REVERT: E 90 MET cc_start: 0.7309 (tpp) cc_final: 0.6905 (mpp) REVERT: E 96 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7632 (m) REVERT: E 131 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7599 (mtt180) REVERT: F 84 MET cc_start: 0.7334 (mmm) cc_final: 0.6946 (mmm) REVERT: G 36 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8354 (mmmm) REVERT: G 62 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7245 (tt) REVERT: G 74 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8308 (mtpp) REVERT: W 275 GLU cc_start: 0.6208 (tp30) cc_final: 0.5658 (tp30) REVERT: W 278 MET cc_start: 0.4793 (mmm) cc_final: 0.4514 (mmm) REVERT: W 320 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6662 (mt) REVERT: W 323 LYS cc_start: 0.7239 (tttt) cc_final: 0.6356 (ptmt) REVERT: W 393 ARG cc_start: 0.7527 (ptp90) cc_final: 0.7295 (ttp-110) REVERT: W 412 LYS cc_start: 0.6710 (tttm) cc_final: 0.6358 (ttpt) REVERT: W 434 GLN cc_start: 0.6169 (tp-100) cc_final: 0.5931 (tp40) REVERT: W 507 GLU cc_start: 0.6931 (tt0) cc_final: 0.6241 (tt0) REVERT: W 513 THR cc_start: 0.6960 (p) cc_final: 0.6661 (t) REVERT: W 547 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7812 (ttp-110) REVERT: W 556 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7495 (mmm) REVERT: W 565 ILE cc_start: 0.7197 (mm) cc_final: 0.6951 (mp) REVERT: W 568 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7556 (mtm-85) REVERT: W 570 MET cc_start: 0.7376 (tpp) cc_final: 0.6958 (mpp) REVERT: W 598 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7905 (ttmm) REVERT: W 599 ASP cc_start: 0.7609 (m-30) cc_final: 0.7006 (m-30) REVERT: W 615 GLU cc_start: 0.7931 (mp0) cc_final: 0.7381 (mp0) REVERT: W 629 THR cc_start: 0.8262 (t) cc_final: 0.7981 (m) REVERT: W 652 GLU cc_start: 0.7464 (tt0) cc_final: 0.7140 (pt0) REVERT: W 695 LEU cc_start: 0.7226 (mt) cc_final: 0.6765 (mp) REVERT: W 732 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7946 (mtp85) REVERT: W 754 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7010 (mm-30) REVERT: W 757 LYS cc_start: 0.8121 (mttt) cc_final: 0.7331 (mttt) REVERT: W 766 LYS cc_start: 0.6123 (pttt) cc_final: 0.5872 (pttp) REVERT: W 914 THR cc_start: 0.5660 (OUTLIER) cc_final: 0.5086 (p) REVERT: W 1060 ARG cc_start: 0.7136 (tpp-160) cc_final: 0.6283 (tpp-160) REVERT: W 1065 GLU cc_start: 0.7096 (pp20) cc_final: 0.6498 (pp20) REVERT: W 1069 MET cc_start: 0.6849 (mmm) cc_final: 0.6611 (mmm) outliers start: 31 outliers final: 10 residues processed: 212 average time/residue: 0.4100 time to fit residues: 121.9888 Evaluate side-chains 212 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 755 LEU Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 74 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 162 optimal weight: 30.0000 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 444 ASN ** W 578 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 = 0.4129 r_free = 0.4129 target = 0.174751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132073 restraints weight = 27663.494| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.69 r_work: 0.3467 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19485 Z= 0.175 Angle : 0.553 10.087 27619 Z= 0.324 Chirality : 0.037 0.153 3067 Planarity : 0.004 0.042 2430 Dihedral : 28.528 175.975 5062 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.34 % Allowed : 15.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1462 helix: 1.67 (0.18), residues: 833 sheet: 0.02 (0.77), residues: 56 loop : -0.91 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.025 0.001 PHE W 748 TYR 0.028 0.001 TYR W 374 ARG 0.006 0.000 ARG W 572 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 902) hydrogen bonds : angle 3.39643 ( 2362) covalent geometry : bond 0.00391 (19485) covalent geometry : angle 0.55347 (27619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7020 (ttp-170) REVERT: C 72 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: C 88 ARG cc_start: 0.8914 (mmt-90) cc_final: 0.8652 (mmt180) REVERT: C 95 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8247 (ttmm) REVERT: D 56 MET cc_start: 0.7895 (mmm) cc_final: 0.7686 (tpp) REVERT: E 77 ASP cc_start: 0.8287 (t0) cc_final: 0.7985 (t0) REVERT: E 90 MET cc_start: 0.7311 (tpp) cc_final: 0.6945 (mpp) REVERT: E 96 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7667 (m) REVERT: E 131 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7608 (mtt180) REVERT: F 84 MET cc_start: 0.7281 (mmm) cc_final: 0.6847 (mmm) REVERT: G 62 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7364 (tt) REVERT: G 74 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8359 (mtpp) REVERT: W 275 GLU cc_start: 0.6122 (tp30) cc_final: 0.5586 (tp30) REVERT: W 278 MET cc_start: 0.4972 (mmm) cc_final: 0.4565 (mmm) REVERT: W 320 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6262 (mt) REVERT: W 323 LYS cc_start: 0.7494 (tttt) cc_final: 0.6615 (ptmt) REVERT: W 412 LYS cc_start: 0.6723 (tttm) cc_final: 0.6416 (ttpt) REVERT: W 413 TRP cc_start: 0.7732 (m-90) cc_final: 0.5966 (m-90) REVERT: W 423 TRP cc_start: 0.6931 (m100) cc_final: 0.6729 (m100) REVERT: W 434 GLN cc_start: 0.6024 (tp-100) cc_final: 0.5745 (tp40) REVERT: W 507 GLU cc_start: 0.7012 (tt0) cc_final: 0.6252 (tt0) REVERT: W 527 HIS cc_start: 0.7674 (m-70) cc_final: 0.7102 (m-70) REVERT: W 545 TRP cc_start: 0.8350 (m100) cc_final: 0.7964 (m100) REVERT: W 547 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7852 (ttp-110) REVERT: W 556 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (mmm) REVERT: W 568 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7883 (mtm-85) REVERT: W 570 MET cc_start: 0.7462 (tpp) cc_final: 0.7051 (mpp) REVERT: W 598 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7941 (ttmm) REVERT: W 599 ASP cc_start: 0.7700 (m-30) cc_final: 0.7317 (m-30) REVERT: W 614 ASP cc_start: 0.7966 (t0) cc_final: 0.7701 (t0) REVERT: W 629 THR cc_start: 0.8245 (t) cc_final: 0.7966 (m) REVERT: W 652 GLU cc_start: 0.7325 (tt0) cc_final: 0.7069 (pt0) REVERT: W 754 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7051 (mm-30) REVERT: W 757 LYS cc_start: 0.8152 (mttt) cc_final: 0.7342 (mttt) REVERT: W 964 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: W 1060 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.6558 (tpp-160) REVERT: W 1065 GLU cc_start: 0.7200 (pp20) cc_final: 0.6540 (pp20) REVERT: W 1069 MET cc_start: 0.6873 (mmm) cc_final: 0.6653 (mmm) outliers start: 30 outliers final: 16 residues processed: 219 average time/residue: 0.3945 time to fit residues: 120.5410 Evaluate side-chains 221 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 424 GLU Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 141 optimal weight: 0.0470 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 60 ASN ** W 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 587 ASN W 647 GLN W 722 GLN W 761 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127193 restraints weight = 27679.697| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.71 r_work: 0.3396 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19485 Z= 0.275 Angle : 0.627 9.981 27619 Z= 0.363 Chirality : 0.043 0.154 3067 Planarity : 0.004 0.052 2430 Dihedral : 28.749 175.557 5062 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.81 % Allowed : 15.37 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1462 helix: 1.43 (0.18), residues: 835 sheet: -0.10 (0.76), residues: 56 loop : -1.01 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP W 491 HIS 0.009 0.001 HIS W 579 PHE 0.026 0.002 PHE W 748 TYR 0.028 0.002 TYR W 374 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 902) hydrogen bonds : angle 3.57406 ( 2362) covalent geometry : bond 0.00632 (19485) covalent geometry : angle 0.62738 (27619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7640 (mp) REVERT: C 29 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7005 (ttp-170) REVERT: C 88 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8603 (mmt180) REVERT: C 95 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8270 (ttmm) REVERT: D 56 MET cc_start: 0.7948 (mmm) cc_final: 0.7696 (mmm) REVERT: D 90 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: E 77 ASP cc_start: 0.8283 (t0) cc_final: 0.7973 (t0) REVERT: E 90 MET cc_start: 0.7277 (tpp) cc_final: 0.7000 (mpp) REVERT: E 96 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7687 (m) REVERT: E 131 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7587 (mtt180) REVERT: F 84 MET cc_start: 0.7382 (mmm) cc_final: 0.7007 (mmm) REVERT: G 62 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7445 (tt) REVERT: G 74 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8331 (mtpp) REVERT: W 278 MET cc_start: 0.5153 (mmm) cc_final: 0.4629 (mmm) REVERT: W 279 ASP cc_start: 0.4786 (t0) cc_final: 0.4391 (t0) REVERT: W 320 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6353 (mt) REVERT: W 323 LYS cc_start: 0.7594 (tttt) cc_final: 0.7104 (ptmt) REVERT: W 340 GLN cc_start: 0.8389 (pp30) cc_final: 0.8184 (pp30) REVERT: W 410 TYR cc_start: 0.5268 (OUTLIER) cc_final: 0.4739 (t80) REVERT: W 412 LYS cc_start: 0.6716 (tttm) cc_final: 0.6218 (ttpt) REVERT: W 477 GLU cc_start: 0.7755 (mp0) cc_final: 0.7533 (mp0) REVERT: W 507 GLU cc_start: 0.7048 (tt0) cc_final: 0.6275 (tt0) REVERT: W 527 HIS cc_start: 0.7612 (m-70) cc_final: 0.6988 (m170) REVERT: W 547 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.7828 (ttp-110) REVERT: W 556 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7632 (mmm) REVERT: W 568 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7835 (mtm-85) REVERT: W 570 MET cc_start: 0.7458 (tpp) cc_final: 0.7023 (mpp) REVERT: W 589 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.6172 (tt) REVERT: W 598 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8036 (ttmm) REVERT: W 614 ASP cc_start: 0.8059 (t0) cc_final: 0.7757 (t0) REVERT: W 629 THR cc_start: 0.8254 (t) cc_final: 0.7992 (m) REVERT: W 695 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7021 (tp) REVERT: W 721 LEU cc_start: 0.8212 (mt) cc_final: 0.8011 (tp) REVERT: W 753 MET cc_start: 0.7847 (mmm) cc_final: 0.7601 (mmm) REVERT: W 754 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7025 (mm-30) REVERT: W 757 LYS cc_start: 0.8190 (mttt) cc_final: 0.7344 (mttt) REVERT: W 766 LYS cc_start: 0.6470 (pttt) cc_final: 0.6092 (pttp) REVERT: W 963 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7450 (mt-10) REVERT: W 1056 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6859 (mm-30) REVERT: W 1060 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.6755 (tpp-160) REVERT: W 1061 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7391 (pp30) REVERT: W 1065 GLU cc_start: 0.7246 (pp20) cc_final: 0.6486 (pp20) REVERT: W 1069 MET cc_start: 0.6946 (mmm) cc_final: 0.6660 (mmm) outliers start: 36 outliers final: 17 residues processed: 224 average time/residue: 0.4137 time to fit residues: 129.3766 Evaluate side-chains 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 590 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 695 LEU Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 118 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN W 341 GLN ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 782 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.170997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128423 restraints weight = 27252.361| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.68 r_work: 0.3414 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19485 Z= 0.235 Angle : 0.596 11.064 27619 Z= 0.346 Chirality : 0.040 0.185 3067 Planarity : 0.004 0.045 2430 Dihedral : 28.714 176.492 5062 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.28 % Allowed : 15.05 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1462 helix: 1.51 (0.18), residues: 830 sheet: -0.33 (0.75), residues: 56 loop : -1.00 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 491 HIS 0.008 0.001 HIS W 675 PHE 0.020 0.001 PHE W 748 TYR 0.023 0.002 TYR W 374 ARG 0.007 0.000 ARG W 572 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 902) hydrogen bonds : angle 3.47922 ( 2362) covalent geometry : bond 0.00538 (19485) covalent geometry : angle 0.59632 (27619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7021 (ttp-170) REVERT: C 88 ARG cc_start: 0.8891 (mmt-90) cc_final: 0.8625 (mmt180) REVERT: C 95 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8284 (ttmm) REVERT: D 90 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: E 77 ASP cc_start: 0.8266 (t0) cc_final: 0.7963 (t0) REVERT: E 90 MET cc_start: 0.7227 (tpp) cc_final: 0.6951 (mpp) REVERT: E 96 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7683 (m) REVERT: E 131 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7618 (mtt180) REVERT: F 50 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7800 (tp) REVERT: F 84 MET cc_start: 0.7354 (mmm) cc_final: 0.6961 (mmm) REVERT: G 74 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8325 (mtpp) REVERT: W 278 MET cc_start: 0.5136 (mmm) cc_final: 0.4609 (mmm) REVERT: W 279 ASP cc_start: 0.4549 (t0) cc_final: 0.3475 (t0) REVERT: W 320 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6346 (mt) REVERT: W 323 LYS cc_start: 0.7605 (tttt) cc_final: 0.7122 (ptmt) REVERT: W 406 TYR cc_start: 0.5790 (t80) cc_final: 0.5574 (t80) REVERT: W 410 TYR cc_start: 0.4906 (OUTLIER) cc_final: 0.4621 (t80) REVERT: W 413 TRP cc_start: 0.7846 (m-90) cc_final: 0.6337 (m-90) REVERT: W 423 TRP cc_start: 0.6961 (m100) cc_final: 0.6714 (m100) REVERT: W 477 GLU cc_start: 0.7684 (mp0) cc_final: 0.7350 (mp0) REVERT: W 482 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7493 (mmt-90) REVERT: W 485 GLN cc_start: 0.8120 (mp10) cc_final: 0.7901 (mp10) REVERT: W 507 GLU cc_start: 0.7033 (tt0) cc_final: 0.6272 (tt0) REVERT: W 527 HIS cc_start: 0.7635 (m-70) cc_final: 0.6929 (m-70) REVERT: W 542 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8081 (tp) REVERT: W 547 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7843 (ttp-110) REVERT: W 550 GLN cc_start: 0.8412 (mt0) cc_final: 0.8168 (mm110) REVERT: W 568 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7878 (mtm-85) REVERT: W 570 MET cc_start: 0.7557 (tpp) cc_final: 0.7167 (mpp) REVERT: W 580 GLN cc_start: 0.6477 (mp-120) cc_final: 0.6002 (mp-120) REVERT: W 589 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.6205 (tt) REVERT: W 598 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7908 (ttmm) REVERT: W 614 ASP cc_start: 0.8074 (t0) cc_final: 0.7788 (t0) REVERT: W 629 THR cc_start: 0.8259 (t) cc_final: 0.8006 (m) REVERT: W 665 PHE cc_start: 0.6950 (m-80) cc_final: 0.6463 (m-80) REVERT: W 721 LEU cc_start: 0.8270 (mt) cc_final: 0.8058 (tp) REVERT: W 754 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7690 (mm-30) REVERT: W 766 LYS cc_start: 0.6419 (pttt) cc_final: 0.5940 (pttp) REVERT: W 963 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7508 (mt-10) REVERT: W 1056 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6969 (mm-30) REVERT: W 1059 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: W 1060 ARG cc_start: 0.7627 (tpp-160) cc_final: 0.6842 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7107 (mm-30) REVERT: W 1069 MET cc_start: 0.6993 (mmm) cc_final: 0.6710 (mmm) outliers start: 42 outliers final: 22 residues processed: 231 average time/residue: 0.3959 time to fit residues: 127.7340 Evaluate side-chains 232 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 542 LEU Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 562 LEU Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 590 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Chi-restraints excluded: chain W residue 1059 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN W 578 HIS ** W 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 724 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132368 restraints weight = 27293.239| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.71 r_work: 0.3466 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19485 Z= 0.155 Angle : 0.550 10.568 27619 Z= 0.318 Chirality : 0.036 0.171 3067 Planarity : 0.004 0.047 2430 Dihedral : 28.531 174.849 5062 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.34 % Allowed : 16.30 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1462 helix: 1.73 (0.18), residues: 839 sheet: -0.33 (0.75), residues: 56 loop : -0.94 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.008 0.001 PHE W 519 TYR 0.030 0.001 TYR W 484 ARG 0.007 0.000 ARG W 572 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 902) hydrogen bonds : angle 3.31303 ( 2362) covalent geometry : bond 0.00342 (19485) covalent geometry : angle 0.54974 (27619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7903 (mmm) cc_final: 0.7614 (mmm) REVERT: C 29 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6937 (ttp-170) REVERT: C 88 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8676 (mpt180) REVERT: D 56 MET cc_start: 0.7848 (mmm) cc_final: 0.7630 (tpp) REVERT: D 90 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: D 120 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8253 (p) REVERT: E 77 ASP cc_start: 0.8292 (t0) cc_final: 0.7996 (t0) REVERT: E 90 MET cc_start: 0.7252 (tpp) cc_final: 0.6908 (mpp) REVERT: E 96 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7667 (m) REVERT: E 131 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7614 (mtt180) REVERT: F 84 MET cc_start: 0.7244 (mmm) cc_final: 0.6840 (mmm) REVERT: G 62 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7283 (tt) REVERT: G 74 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8368 (mtpp) REVERT: W 278 MET cc_start: 0.5151 (mmm) cc_final: 0.4630 (mmm) REVERT: W 279 ASP cc_start: 0.4731 (t0) cc_final: 0.3549 (t0) REVERT: W 320 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6284 (mt) REVERT: W 323 LYS cc_start: 0.7585 (tttt) cc_final: 0.7097 (ptmt) REVERT: W 378 GLN cc_start: 0.8406 (mp10) cc_final: 0.8206 (pm20) REVERT: W 406 TYR cc_start: 0.5535 (t80) cc_final: 0.5318 (t80) REVERT: W 410 TYR cc_start: 0.4671 (OUTLIER) cc_final: 0.4314 (t80) REVERT: W 413 TRP cc_start: 0.7693 (m-90) cc_final: 0.6053 (m-90) REVERT: W 482 ARG cc_start: 0.7838 (mmt-90) cc_final: 0.7413 (mmt-90) REVERT: W 485 GLN cc_start: 0.7958 (mp10) cc_final: 0.7709 (mp10) REVERT: W 507 GLU cc_start: 0.6995 (tt0) cc_final: 0.6448 (tt0) REVERT: W 513 THR cc_start: 0.7014 (p) cc_final: 0.6484 (t) REVERT: W 550 GLN cc_start: 0.8417 (mt0) cc_final: 0.8175 (mm110) REVERT: W 570 MET cc_start: 0.7738 (tpp) cc_final: 0.7371 (mpp) REVERT: W 598 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7796 (ttmm) REVERT: W 599 ASP cc_start: 0.7674 (m-30) cc_final: 0.7210 (m-30) REVERT: W 614 ASP cc_start: 0.8043 (t0) cc_final: 0.7782 (t0) REVERT: W 629 THR cc_start: 0.8256 (t) cc_final: 0.7996 (m) REVERT: W 732 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7757 (ttp-110) REVERT: W 753 MET cc_start: 0.8020 (mmm) cc_final: 0.7753 (mmm) REVERT: W 754 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7581 (mm-30) REVERT: W 963 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7530 (mt-10) REVERT: W 1056 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7084 (mm-30) REVERT: W 1058 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6238 (tm-30) REVERT: W 1059 GLU cc_start: 0.8057 (tp30) cc_final: 0.7177 (mp0) REVERT: W 1060 ARG cc_start: 0.7679 (tpp-160) cc_final: 0.6900 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7120 (mm-30) REVERT: W 1069 MET cc_start: 0.7010 (mmm) cc_final: 0.6754 (mmm) outliers start: 30 outliers final: 13 residues processed: 218 average time/residue: 0.4162 time to fit residues: 126.2322 Evaluate side-chains 217 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 930 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 151 optimal weight: 0.5980 chunk 146 optimal weight: 0.0040 chunk 25 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 104 optimal weight: 0.0570 chunk 110 optimal weight: 0.0040 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN W 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137379 restraints weight = 27475.246| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.65 r_work: 0.3545 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19485 Z= 0.131 Angle : 0.535 10.187 27619 Z= 0.308 Chirality : 0.035 0.167 3067 Planarity : 0.004 0.046 2430 Dihedral : 28.385 175.954 5062 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 16.77 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1462 helix: 1.97 (0.18), residues: 847 sheet: -0.27 (0.74), residues: 56 loop : -0.87 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 491 HIS 0.006 0.001 HIS C 82 PHE 0.012 0.001 PHE W 773 TYR 0.025 0.001 TYR W 763 ARG 0.006 0.000 ARG W 572 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 902) hydrogen bonds : angle 3.19219 ( 2362) covalent geometry : bond 0.00281 (19485) covalent geometry : angle 0.53477 (27619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7902 (mmm) cc_final: 0.7640 (mmm) REVERT: C 29 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: D 56 MET cc_start: 0.7805 (mmm) cc_final: 0.7525 (tpp) REVERT: D 90 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: D 120 SER cc_start: 0.8754 (m) cc_final: 0.8251 (p) REVERT: E 77 ASP cc_start: 0.8295 (t0) cc_final: 0.8006 (t0) REVERT: E 90 MET cc_start: 0.7254 (tpp) cc_final: 0.6863 (mpp) REVERT: E 131 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7621 (mtt180) REVERT: F 84 MET cc_start: 0.7118 (mmm) cc_final: 0.6800 (mmm) REVERT: G 74 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8412 (mtpp) REVERT: W 278 MET cc_start: 0.5125 (mmm) cc_final: 0.4583 (mmm) REVERT: W 279 ASP cc_start: 0.4727 (t0) cc_final: 0.3419 (t0) REVERT: W 320 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6133 (mt) REVERT: W 323 LYS cc_start: 0.7623 (tttt) cc_final: 0.7158 (ptmt) REVERT: W 410 TYR cc_start: 0.4462 (OUTLIER) cc_final: 0.4215 (t80) REVERT: W 482 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7521 (mmt-90) REVERT: W 507 GLU cc_start: 0.6893 (tt0) cc_final: 0.6299 (tt0) REVERT: W 545 TRP cc_start: 0.8267 (m100) cc_final: 0.7828 (m100) REVERT: W 550 GLN cc_start: 0.8350 (mt0) cc_final: 0.8109 (mm-40) REVERT: W 570 MET cc_start: 0.7731 (tpp) cc_final: 0.7318 (mpp) REVERT: W 598 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7860 (ttmm) REVERT: W 599 ASP cc_start: 0.7898 (m-30) cc_final: 0.7631 (m-30) REVERT: W 614 ASP cc_start: 0.8043 (t0) cc_final: 0.7771 (t0) REVERT: W 629 THR cc_start: 0.8243 (t) cc_final: 0.7992 (m) REVERT: W 693 PHE cc_start: 0.6809 (m-80) cc_final: 0.6414 (m-80) REVERT: W 753 MET cc_start: 0.7996 (mmm) cc_final: 0.7649 (mmm) REVERT: W 754 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7686 (mm-30) REVERT: W 963 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7478 (mt-10) REVERT: W 1056 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7119 (mm-30) REVERT: W 1058 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6280 (tm-30) REVERT: W 1059 GLU cc_start: 0.8064 (tp30) cc_final: 0.7148 (mp0) REVERT: W 1060 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.6901 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7104 (mm-30) REVERT: W 1069 MET cc_start: 0.6951 (mmm) cc_final: 0.6676 (mmm) outliers start: 23 outliers final: 14 residues processed: 215 average time/residue: 0.4039 time to fit residues: 121.0435 Evaluate side-chains 210 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 751 ILE Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 930 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 172 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS G 73 ASN ** W 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 580 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 = 0.4120 r_free = 0.4120 target = 0.173626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130888 restraints weight = 27279.800| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.63 r_work: 0.3449 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19485 Z= 0.218 Angle : 0.598 10.069 27619 Z= 0.343 Chirality : 0.039 0.217 3067 Planarity : 0.004 0.058 2430 Dihedral : 28.622 175.249 5062 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.72 % Allowed : 17.39 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1462 helix: 1.66 (0.18), residues: 846 sheet: -0.23 (0.75), residues: 56 loop : -0.93 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 413 HIS 0.007 0.001 HIS W 675 PHE 0.017 0.001 PHE H 67 TYR 0.035 0.002 TYR W 484 ARG 0.006 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 902) hydrogen bonds : angle 3.40842 ( 2362) covalent geometry : bond 0.00497 (19485) covalent geometry : angle 0.59822 (27619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7887 (mmm) cc_final: 0.7506 (mmm) REVERT: C 29 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7027 (ttp-170) REVERT: C 88 ARG cc_start: 0.8883 (mmt-90) cc_final: 0.8655 (mmt180) REVERT: D 56 MET cc_start: 0.7877 (mmm) cc_final: 0.7635 (mmm) REVERT: D 90 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6916 (mt-10) REVERT: D 120 SER cc_start: 0.8849 (m) cc_final: 0.8380 (p) REVERT: E 77 ASP cc_start: 0.8269 (t0) cc_final: 0.7998 (t0) REVERT: E 90 MET cc_start: 0.7280 (tpp) cc_final: 0.7012 (mpp) REVERT: E 131 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7593 (mtt180) REVERT: F 84 MET cc_start: 0.7273 (mmm) cc_final: 0.7006 (mmm) REVERT: W 278 MET cc_start: 0.5142 (mmm) cc_final: 0.4617 (mmm) REVERT: W 279 ASP cc_start: 0.5203 (t0) cc_final: 0.3460 (t0) REVERT: W 320 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6311 (mt) REVERT: W 323 LYS cc_start: 0.7662 (tttt) cc_final: 0.7198 (ptmt) REVERT: W 387 GLN cc_start: 0.8124 (mt0) cc_final: 0.6996 (tp40) REVERT: W 413 TRP cc_start: 0.7594 (m-90) cc_final: 0.6184 (m-90) REVERT: W 418 TYR cc_start: 0.7901 (m-10) cc_final: 0.7579 (m-80) REVERT: W 420 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7560 (mm-30) REVERT: W 482 ARG cc_start: 0.7719 (mmt-90) cc_final: 0.7493 (mmt-90) REVERT: W 507 GLU cc_start: 0.7197 (tt0) cc_final: 0.6513 (tt0) REVERT: W 542 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8046 (tp) REVERT: W 545 TRP cc_start: 0.8353 (m100) cc_final: 0.8001 (m100) REVERT: W 550 GLN cc_start: 0.8395 (mt0) cc_final: 0.8140 (mm110) REVERT: W 568 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7678 (mtm-85) REVERT: W 570 MET cc_start: 0.7746 (tpp) cc_final: 0.7322 (mpp) REVERT: W 598 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7837 (ttmm) REVERT: W 599 ASP cc_start: 0.7838 (m-30) cc_final: 0.7377 (m-30) REVERT: W 614 ASP cc_start: 0.8024 (t0) cc_final: 0.7739 (t0) REVERT: W 629 THR cc_start: 0.8286 (t) cc_final: 0.8022 (m) REVERT: W 715 ARG cc_start: 0.7330 (ptm-80) cc_final: 0.7102 (ptm-80) REVERT: W 727 LYS cc_start: 0.7307 (tptt) cc_final: 0.7078 (tppt) REVERT: W 732 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.7858 (ttp-110) REVERT: W 753 MET cc_start: 0.8039 (mmm) cc_final: 0.7791 (mmm) REVERT: W 754 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7602 (mm-30) REVERT: W 963 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7588 (mt-10) REVERT: W 1056 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7235 (mm-30) REVERT: W 1058 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6277 (tm-30) REVERT: W 1059 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: W 1060 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.6974 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7168 (mm-30) REVERT: W 1069 MET cc_start: 0.6977 (mmm) cc_final: 0.6700 (mmm) outliers start: 22 outliers final: 12 residues processed: 204 average time/residue: 0.4111 time to fit residues: 117.0635 Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 542 LEU Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 590 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 930 MET Chi-restraints excluded: chain W residue 990 MET Chi-restraints excluded: chain W residue 1059 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 169 optimal weight: 0.8980 chunk 143 optimal weight: 0.0570 chunk 51 optimal weight: 0.3980 chunk 69 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 168 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 overall best weight: 0.2748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** W 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 485 GLN ** W 580 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 = 0.4190 r_free = 0.4190 target = 0.179676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137520 restraints weight = 27409.824| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.66 r_work: 0.3544 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19485 Z= 0.132 Angle : 0.545 9.792 27619 Z= 0.312 Chirality : 0.035 0.287 3067 Planarity : 0.004 0.060 2430 Dihedral : 28.348 175.595 5062 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.25 % Allowed : 18.10 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1462 helix: 2.02 (0.18), residues: 843 sheet: -0.05 (0.74), residues: 56 loop : -0.89 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP W 491 HIS 0.007 0.001 HIS W 579 PHE 0.010 0.001 PHE W 829 TYR 0.035 0.001 TYR W 484 ARG 0.014 0.000 ARG W 827 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 902) hydrogen bonds : angle 3.18923 ( 2362) covalent geometry : bond 0.00285 (19485) covalent geometry : angle 0.54530 (27619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11176.18 seconds wall clock time: 191 minutes 52.58 seconds (11512.58 seconds total)