Starting phenix.real_space_refine on Mon May 19 06:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nh8_49406/05_2025/9nh8_49406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nh8_49406/05_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_49406/05_2025/9nh8_49406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nh8_49406/05_2025/9nh8_49406.map" model { file = "/net/cci-nas-00/data/ceres_data/9nh8_49406/05_2025/9nh8_49406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nh8_49406/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.65, per 1000 atoms: 0.52 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: 4.08 Conformation dependent library (CDL) restraints added in 1.5 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: 5.70 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: 8.90 Time building geometry restraints manager: 4.84 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: 1.430 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.260 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.050 ------------------------------------------------------------------------------- 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 : 1.397 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: 0.3580 time to fit residues: 124.8300 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 : 1.355 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.178756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135712 restraints weight = 27703.783| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.75 r_work: 0.3496 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4064 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 : 7.39 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 0.05325 ( 902) hydrogen bonds : angle 4.03062 ( 2362) covalent geometry : bond 0.00568 (19485) covalent geometry : angle 0.69848 (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 : 1.436 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: 0.7934 (mmm) cc_final: 0.7654 (tpp) REVERT: C 29 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6685 (ttp-170) REVERT: C 95 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8324 (ttmm) REVERT: E 77 ASP cc_start: 0.8293 (t0) cc_final: 0.8085 (t0) REVERT: E 90 MET cc_start: 0.7319 (tpp) cc_final: 0.6886 (mpp) REVERT: F 84 MET cc_start: 0.7325 (mmm) cc_final: 0.7004 (mmm) REVERT: G 36 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8243 (mmmm) REVERT: G 74 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8300 (mtpp) REVERT: H 56 MET cc_start: 0.7991 (mmm) cc_final: 0.7622 (mmm) REVERT: W 276 ARG cc_start: 0.6403 (ttt180) cc_final: 0.5715 (ttt90) REVERT: W 278 MET cc_start: 0.4394 (mmm) cc_final: 0.4109 (mmm) REVERT: W 317 GLN cc_start: 0.5396 (mm-40) cc_final: 0.4904 (mm-40) REVERT: W 318 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5834 (p90) REVERT: W 319 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.2321 (mt) REVERT: W 323 LYS cc_start: 0.7103 (tttt) cc_final: 0.6703 (ttpt) REVERT: W 353 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8045 (mtmm) REVERT: W 412 LYS cc_start: 0.6866 (tttm) cc_final: 0.6653 (ttmt) REVERT: W 507 GLU cc_start: 0.6930 (tt0) cc_final: 0.6280 (tt0) REVERT: W 568 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7785 (mtm-85) REVERT: W 570 MET cc_start: 0.7495 (tpp) cc_final: 0.7087 (mpp) REVERT: W 615 GLU cc_start: 0.7805 (mp0) cc_final: 0.7482 (mp0) REVERT: W 627 TYR cc_start: 0.8303 (t80) cc_final: 0.7480 (t80) REVERT: W 629 THR cc_start: 0.8253 (t) cc_final: 0.7926 (m) REVERT: W 816 MET cc_start: 0.7648 (tpt) cc_final: 0.7142 (tpt) REVERT: W 920 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6248 (tm-30) REVERT: W 1050 ASP cc_start: 0.7219 (p0) cc_final: 0.6550 (t0) REVERT: W 1059 GLU cc_start: 0.6963 (tp30) cc_final: 0.6485 (tp30) REVERT: W 1062 LYS cc_start: 0.6392 (ttpt) cc_final: 0.6185 (ttpt) REVERT: W 1069 MET cc_start: 0.6563 (mmm) cc_final: 0.6363 (mmm) outliers start: 31 outliers final: 14 residues processed: 220 average time/residue: 0.3900 time to fit residues: 119.8962 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 : 1.357 ------------------------------------------------------------------------------- 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: 0.9980 chunk 57 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.177818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134937 restraints weight = 27541.342| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.74 r_work: 0.3498 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19485 Z= 0.172 Angle : 0.567 8.291 27619 Z= 0.332 Chirality : 0.037 0.142 3067 Planarity : 0.004 0.040 2430 Dihedral : 28.718 178.054 5064 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.87 % Allowed : 14.27 % Favored : 83.85 % 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: 0.56 (0.22), residues: 1462 helix: 1.28 (0.18), residues: 834 sheet: -0.52 (0.73), residues: 61 loop : -0.86 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.039 0.001 PHE W 748 TYR 0.015 0.001 TYR F 98 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 902) hydrogen bonds : angle 3.61051 ( 2362) covalent geometry : bond 0.00379 (19485) covalent geometry : angle 0.56707 (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 216 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.450 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: 0.8038 (OUTLIER) cc_final: 0.6935 (ttp-170) REVERT: E 77 ASP cc_start: 0.8286 (t0) cc_final: 0.8021 (t0) REVERT: E 90 MET cc_start: 0.7364 (tpp) cc_final: 0.6973 (mpp) REVERT: F 84 MET cc_start: 0.7383 (mmm) cc_final: 0.7022 (mmm) REVERT: G 36 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8302 (mmmm) REVERT: G 74 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8346 (mtpp) REVERT: W 276 ARG cc_start: 0.6400 (ttt180) cc_final: 0.5593 (ttt90) REVERT: W 278 MET cc_start: 0.4611 (mmm) cc_final: 0.4291 (mmm) REVERT: W 317 GLN cc_start: 0.5151 (mm-40) cc_final: 0.4859 (mm-40) REVERT: W 319 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.2317 (mt) REVERT: W 320 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6868 (mt) REVERT: W 323 LYS cc_start: 0.7249 (tttt) cc_final: 0.6837 (ptmt) REVERT: W 393 ARG cc_start: 0.7510 (ptp90) cc_final: 0.7250 (ttp-110) REVERT: W 412 LYS cc_start: 0.6847 (tttm) cc_final: 0.6502 (ttpt) REVERT: W 507 GLU cc_start: 0.7014 (tt0) cc_final: 0.6250 (tt0) REVERT: W 568 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7477 (mtm-85) REVERT: W 570 MET cc_start: 0.7467 (tpp) cc_final: 0.7065 (mpp) REVERT: W 599 ASP cc_start: 0.7661 (m-30) cc_final: 0.7114 (m-30) REVERT: W 629 THR cc_start: 0.8259 (t) cc_final: 0.7958 (m) REVERT: W 652 GLU cc_start: 0.7499 (tt0) cc_final: 0.7173 (pt0) REVERT: W 690 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7460 (pp) REVERT: W 757 LYS cc_start: 0.8080 (mttt) cc_final: 0.7570 (mttt) REVERT: W 921 ASP cc_start: 0.6581 (m-30) cc_final: 0.6370 (m-30) REVERT: W 964 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: W 1050 ASP cc_start: 0.7257 (p0) cc_final: 0.6767 (t70) REVERT: W 1069 MET cc_start: 0.6960 (mmm) cc_final: 0.6674 (mmm) outliers start: 24 outliers final: 8 residues processed: 208 average time/residue: 0.3864 time to fit residues: 112.4365 Evaluate side-chains 201 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain G residue 36 LYS 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 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: 9.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133176 restraints weight = 27717.301| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.72 r_work: 0.3478 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19485 Z= 0.178 Angle : 0.559 8.142 27619 Z= 0.328 Chirality : 0.037 0.148 3067 Planarity : 0.004 0.040 2430 Dihedral : 28.555 173.754 5064 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.50 % Allowed : 14.51 % Favored : 83.00 % 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: 0.76 (0.22), residues: 1462 helix: 1.50 (0.18), residues: 840 sheet: -0.46 (0.74), residues: 61 loop : -0.90 (0.26), residues: 561 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 0.029 0.001 PHE W 748 TYR 0.027 0.001 TYR W 374 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 902) hydrogen bonds : angle 3.46265 ( 2362) covalent geometry : bond 0.00397 (19485) covalent geometry : angle 0.55856 (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: 32 poor density : 192 time to evaluate : 1.422 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: C 29 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6929 (ttp-170) REVERT: C 72 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: D 56 MET cc_start: 0.7951 (mmm) cc_final: 0.7721 (mmm) REVERT: D 90 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: E 77 ASP cc_start: 0.8282 (t0) cc_final: 0.7995 (t0) REVERT: E 96 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7635 (m) REVERT: E 131 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7617 (mtt180) REVERT: F 84 MET cc_start: 0.7378 (mmm) cc_final: 0.7031 (mmm) REVERT: G 62 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7283 (tt) REVERT: G 74 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8322 (mtpp) REVERT: W 275 GLU cc_start: 0.6236 (tp30) cc_final: 0.5691 (tp30) REVERT: W 278 MET cc_start: 0.4835 (mmm) cc_final: 0.4536 (mmm) REVERT: W 320 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6639 (mt) REVERT: W 323 LYS cc_start: 0.7330 (tttt) cc_final: 0.6445 (ptmt) REVERT: W 393 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7332 (ttp-110) REVERT: W 412 LYS cc_start: 0.6748 (tttm) cc_final: 0.6386 (ttpt) REVERT: W 477 GLU cc_start: 0.7751 (mp0) cc_final: 0.7402 (mp0) REVERT: W 507 GLU cc_start: 0.6927 (tt0) cc_final: 0.6241 (tt0) REVERT: W 513 THR cc_start: 0.6934 (p) cc_final: 0.6621 (t) REVERT: W 547 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7795 (ttp-110) REVERT: W 556 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7471 (mmm) REVERT: W 565 ILE cc_start: 0.7221 (mm) cc_final: 0.6985 (mp) REVERT: W 568 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7788 (mtm-85) REVERT: W 570 MET cc_start: 0.7379 (tpp) cc_final: 0.6929 (mpp) REVERT: W 598 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7928 (ttmm) REVERT: W 599 ASP cc_start: 0.7660 (m-30) cc_final: 0.7246 (m-30) REVERT: W 614 ASP cc_start: 0.7903 (t0) cc_final: 0.7653 (t0) REVERT: W 629 THR cc_start: 0.8262 (t) cc_final: 0.7977 (m) REVERT: W 652 GLU cc_start: 0.7437 (tt0) cc_final: 0.7139 (pt0) REVERT: W 757 LYS cc_start: 0.8124 (mttt) cc_final: 0.7555 (mttt) REVERT: W 766 LYS cc_start: 0.6107 (pttt) cc_final: 0.5899 (pttp) REVERT: W 914 THR cc_start: 0.5705 (OUTLIER) cc_final: 0.5152 (p) REVERT: W 964 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: W 1060 ARG cc_start: 0.7134 (tpp-160) cc_final: 0.6291 (tpp-160) REVERT: W 1069 MET cc_start: 0.6886 (mmm) cc_final: 0.6597 (mmm) outliers start: 32 outliers final: 12 residues processed: 212 average time/residue: 0.4291 time to fit residues: 127.0212 Evaluate side-chains 211 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN 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 72 ASP 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 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 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: 0.7980 chunk 43 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 108 ASN G 73 ASN W 434 GLN W 587 ASN W 722 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.170673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127700 restraints weight = 27594.421| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.70 r_work: 0.3408 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19485 Z= 0.269 Angle : 0.627 9.890 27619 Z= 0.363 Chirality : 0.042 0.190 3067 Planarity : 0.004 0.041 2430 Dihedral : 28.780 174.785 5062 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.81 % Allowed : 15.29 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1462 helix: 1.40 (0.18), residues: 830 sheet: -0.06 (0.77), residues: 56 loop : -1.05 (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 761 PHE 0.027 0.002 PHE W 748 TYR 0.029 0.002 TYR W 374 ARG 0.004 0.000 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.04877 ( 902) hydrogen bonds : angle 3.63173 ( 2362) covalent geometry : bond 0.00621 (19485) covalent geometry : angle 0.62708 (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 241 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7629 (mm) cc_final: 0.7367 (mm) REVERT: A 109 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7572 (mp) REVERT: C 29 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6978 (ttp-170) REVERT: C 72 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: C 88 ARG cc_start: 0.8846 (mmt-90) cc_final: 0.8585 (mmt180) REVERT: D 56 MET cc_start: 0.7940 (mmm) cc_final: 0.7703 (mmm) REVERT: E 77 ASP cc_start: 0.8294 (t0) cc_final: 0.7983 (t0) REVERT: E 90 MET cc_start: 0.7232 (tpp) cc_final: 0.6946 (mpp) REVERT: E 96 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7646 (m) REVERT: E 131 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7613 (mtt180) REVERT: F 84 MET cc_start: 0.7431 (mmm) cc_final: 0.7086 (mmm) REVERT: G 62 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7405 (tt) REVERT: G 74 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8294 (mtpp) REVERT: W 275 GLU cc_start: 0.6259 (tp30) cc_final: 0.5690 (tp30) REVERT: W 278 MET cc_start: 0.5020 (mmm) cc_final: 0.4657 (mmm) REVERT: W 279 ASP cc_start: 0.4805 (t0) cc_final: 0.4597 (t0) REVERT: W 320 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6357 (mt) REVERT: W 323 LYS cc_start: 0.7493 (tttt) cc_final: 0.6571 (ptmt) REVERT: W 412 LYS cc_start: 0.6699 (tttm) cc_final: 0.6285 (ttpt) REVERT: W 413 TRP cc_start: 0.7752 (m-90) cc_final: 0.5947 (m-90) REVERT: W 423 TRP cc_start: 0.6966 (m100) cc_final: 0.6507 (m100) REVERT: W 507 GLU cc_start: 0.7029 (tt0) cc_final: 0.6286 (tt0) REVERT: W 527 HIS cc_start: 0.7605 (m-70) cc_final: 0.7401 (m170) REVERT: W 547 ARG cc_start: 0.8079 (ttp-110) cc_final: 0.7852 (ttp-110) REVERT: W 556 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: W 568 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7708 (mtm-85) REVERT: W 570 MET cc_start: 0.7403 (tpp) cc_final: 0.6974 (mpp) REVERT: W 589 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.6052 (tt) REVERT: W 598 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7914 (ttmm) REVERT: W 614 ASP cc_start: 0.8023 (t0) cc_final: 0.7662 (t0) REVERT: W 629 THR cc_start: 0.8214 (t) cc_final: 0.7961 (m) REVERT: W 754 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7048 (mm-30) REVERT: W 757 LYS cc_start: 0.8110 (mttt) cc_final: 0.7268 (mttt) REVERT: W 761 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.6391 (t-90) REVERT: W 766 LYS cc_start: 0.6406 (pttt) cc_final: 0.6071 (pttp) REVERT: W 964 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: W 1060 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.6553 (tpp-160) REVERT: W 1065 GLU cc_start: 0.7226 (pp20) cc_final: 0.6898 (pp20) REVERT: W 1069 MET cc_start: 0.6863 (mmm) cc_final: 0.6420 (mmm) outliers start: 36 outliers final: 18 residues processed: 227 average time/residue: 0.3882 time to fit residues: 123.0839 Evaluate side-chains 231 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 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 437 ILE 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 761 HIS Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Chi-restraints excluded: chain W residue 990 MET 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: 1.9990 chunk 141 optimal weight: 0.0270 chunk 111 optimal weight: 8.9990 chunk 156 optimal weight: 40.0000 chunk 56 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 chunk 58 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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** E 108 ASN G 73 ASN H 60 ASN W 317 GLN W 444 ASN W 578 HIS ** W 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 647 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132020 restraints weight = 27682.391| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.73 r_work: 0.3457 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5960 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= 0.159 Angle : 0.558 10.652 27619 Z= 0.326 Chirality : 0.036 0.163 3067 Planarity : 0.004 0.042 2430 Dihedral : 28.584 178.453 5062 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.18 % Allowed : 16.38 % 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: 0.90 (0.23), residues: 1462 helix: 1.69 (0.18), residues: 833 sheet: -0.12 (0.76), residues: 56 loop : -0.97 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP W 491 HIS 0.007 0.001 HIS W 579 PHE 0.022 0.001 PHE W 748 TYR 0.019 0.001 TYR W 374 ARG 0.005 0.000 ARG W1053 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 902) hydrogen bonds : angle 3.36337 ( 2362) covalent geometry : bond 0.00350 (19485) covalent geometry : angle 0.55785 (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 225 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7251 (mm) REVERT: B 84 MET cc_start: 0.7861 (mmm) cc_final: 0.7618 (mmm) REVERT: C 29 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6924 (ttp-170) REVERT: C 72 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: D 56 MET cc_start: 0.7860 (mmm) cc_final: 0.7639 (tpp) REVERT: D 90 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: E 77 ASP cc_start: 0.8283 (t0) cc_final: 0.7972 (t0) REVERT: E 90 MET cc_start: 0.7227 (tpp) cc_final: 0.6865 (mpp) REVERT: E 96 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7689 (m) REVERT: F 84 MET cc_start: 0.7309 (mmm) cc_final: 0.7024 (mmm) REVERT: G 74 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8369 (mtpp) REVERT: W 275 GLU cc_start: 0.6052 (tp30) cc_final: 0.5512 (tp30) REVERT: W 278 MET cc_start: 0.5025 (mmm) cc_final: 0.4606 (mmm) REVERT: W 320 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6322 (mt) REVERT: W 323 LYS cc_start: 0.7500 (tttt) cc_final: 0.6638 (ptmt) REVERT: W 406 TYR cc_start: 0.5802 (t80) cc_final: 0.5474 (t80) REVERT: W 410 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.4344 (t80) REVERT: W 412 LYS cc_start: 0.6647 (tttm) cc_final: 0.6316 (ttpt) REVERT: W 432 LYS cc_start: 0.7487 (tptt) cc_final: 0.6750 (ttpt) REVERT: W 477 GLU cc_start: 0.7679 (mp0) cc_final: 0.7463 (mp0) REVERT: W 507 GLU cc_start: 0.7058 (tt0) cc_final: 0.6297 (tt0) REVERT: W 527 HIS cc_start: 0.7621 (m-70) cc_final: 0.7375 (m170) REVERT: W 547 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7818 (ttp-110) REVERT: W 550 GLN cc_start: 0.8359 (mt0) cc_final: 0.8135 (mm110) REVERT: W 568 ARG cc_start: 0.8092 (mtp180) cc_final: 0.6737 (mpp80) REVERT: W 570 MET cc_start: 0.7482 (tpp) cc_final: 0.7088 (mpp) REVERT: W 598 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8009 (ttmm) REVERT: W 599 ASP cc_start: 0.7665 (m-30) cc_final: 0.7386 (m-30) REVERT: W 614 ASP cc_start: 0.8052 (t0) cc_final: 0.7777 (t0) REVERT: W 629 THR cc_start: 0.8226 (t) cc_final: 0.7973 (m) REVERT: W 721 LEU cc_start: 0.8190 (mt) cc_final: 0.7981 (tp) REVERT: W 754 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7600 (mm-30) REVERT: W 766 LYS cc_start: 0.6333 (pttt) cc_final: 0.5923 (pttp) REVERT: W 1056 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6822 (mm-30) REVERT: W 1059 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: W 1060 ARG cc_start: 0.7440 (tpp-160) cc_final: 0.6598 (tpp-160) REVERT: W 1065 GLU cc_start: 0.7295 (pp20) cc_final: 0.6922 (pp20) REVERT: W 1069 MET cc_start: 0.6960 (mmm) cc_final: 0.6472 (mmm) outliers start: 28 outliers final: 9 residues processed: 216 average time/residue: 0.4087 time to fit residues: 122.7326 Evaluate side-chains 213 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 96 SER 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 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 560 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 118 optimal weight: 0.0470 chunk 117 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** W 782 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.178129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135166 restraints weight = 27178.791| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.71 r_work: 0.3489 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.6210 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= 0.145 Angle : 0.538 9.716 27619 Z= 0.313 Chirality : 0.035 0.150 3067 Planarity : 0.004 0.044 2430 Dihedral : 28.434 176.256 5062 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.16 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: 1.10 (0.23), residues: 1462 helix: 1.85 (0.18), residues: 839 sheet: -0.19 (0.76), residues: 56 loop : -0.90 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.020 0.001 PHE W 748 TYR 0.016 0.001 TYR W 374 ARG 0.007 0.000 ARG W 697 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 902) hydrogen bonds : angle 3.27371 ( 2362) covalent geometry : bond 0.00315 (19485) covalent geometry : angle 0.53822 (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 231 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.440 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: 0.7897 (mmm) cc_final: 0.7566 (mmm) REVERT: C 29 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6907 (ttp-170) REVERT: C 72 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: D 56 MET cc_start: 0.7881 (mmm) cc_final: 0.7618 (tpp) REVERT: D 90 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: E 77 ASP cc_start: 0.8295 (t0) cc_final: 0.8023 (t0) REVERT: E 90 MET cc_start: 0.7226 (tpp) cc_final: 0.6835 (mpp) REVERT: E 96 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7646 (m) REVERT: E 131 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7652 (mtt180) REVERT: F 84 MET cc_start: 0.7224 (mmm) cc_final: 0.6832 (mmm) REVERT: G 62 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7269 (tt) REVERT: G 74 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8377 (mtpp) REVERT: W 275 GLU cc_start: 0.5957 (tp30) cc_final: 0.5480 (tp30) REVERT: W 278 MET cc_start: 0.5090 (mmm) cc_final: 0.4572 (mmm) REVERT: W 279 ASP cc_start: 0.4401 (t0) cc_final: 0.3771 (t0) REVERT: W 320 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6217 (mt) REVERT: W 323 LYS cc_start: 0.7527 (tttt) cc_final: 0.6656 (ptmt) REVERT: W 410 TYR cc_start: 0.4733 (OUTLIER) cc_final: 0.4136 (t80) REVERT: W 412 LYS cc_start: 0.6697 (tttm) cc_final: 0.6433 (ttpt) REVERT: W 413 TRP cc_start: 0.7782 (m-90) cc_final: 0.5989 (m-90) REVERT: W 432 LYS cc_start: 0.7376 (tptt) cc_final: 0.6662 (ttpt) REVERT: W 477 GLU cc_start: 0.7690 (mp0) cc_final: 0.7457 (mp0) REVERT: W 507 GLU cc_start: 0.7048 (tt0) cc_final: 0.6510 (tt0) REVERT: W 527 HIS cc_start: 0.7708 (m-70) cc_final: 0.7172 (m-70) REVERT: W 545 TRP cc_start: 0.8370 (m100) cc_final: 0.7542 (m100) REVERT: W 547 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7691 (ttp-110) REVERT: W 570 MET cc_start: 0.7460 (tpp) cc_final: 0.7190 (mpp) REVERT: W 580 GLN cc_start: 0.6494 (mp-120) cc_final: 0.6050 (mp-120) REVERT: W 598 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7936 (ttmm) REVERT: W 599 ASP cc_start: 0.7734 (m-30) cc_final: 0.7445 (m-30) REVERT: W 614 ASP cc_start: 0.8088 (t0) cc_final: 0.7800 (t0) REVERT: W 629 THR cc_start: 0.8238 (t) cc_final: 0.7966 (m) REVERT: W 721 LEU cc_start: 0.8183 (mt) cc_final: 0.7725 (tp) REVERT: W 732 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7974 (ttp-110) REVERT: W 754 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7509 (mm-30) REVERT: W 1056 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6883 (mm-30) REVERT: W 1059 GLU cc_start: 0.7805 (tp30) cc_final: 0.7292 (mp0) REVERT: W 1060 ARG cc_start: 0.7463 (tpp-160) cc_final: 0.6652 (tpp-160) REVERT: W 1065 GLU cc_start: 0.7286 (pp20) cc_final: 0.6492 (pp20) outliers start: 30 outliers final: 16 residues processed: 222 average time/residue: 0.3936 time to fit residues: 121.4213 Evaluate side-chains 216 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 C residue 72 ASP 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 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 476 HIS Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 530 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.175969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133267 restraints weight = 27469.989| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.66 r_work: 0.3483 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19485 Z= 0.169 Angle : 0.558 9.649 27619 Z= 0.321 Chirality : 0.037 0.180 3067 Planarity : 0.004 0.047 2430 Dihedral : 28.482 175.272 5062 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.50 % Allowed : 16.30 % Favored : 81.20 % 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: 1.07 (0.23), residues: 1462 helix: 1.85 (0.18), residues: 833 sheet: -0.25 (0.76), residues: 56 loop : -0.91 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 PHE 0.018 0.001 PHE W 748 TYR 0.029 0.001 TYR W 484 ARG 0.008 0.000 ARG W 572 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 902) hydrogen bonds : angle 3.31222 ( 2362) covalent geometry : bond 0.00377 (19485) covalent geometry : angle 0.55815 (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 228 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.415 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: B 84 MET cc_start: 0.7893 (mmm) cc_final: 0.7491 (mmm) REVERT: C 29 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6988 (ttp-170) REVERT: C 88 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8640 (mmt180) REVERT: D 56 MET cc_start: 0.7877 (mmm) cc_final: 0.7663 (tpp) REVERT: D 90 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: E 77 ASP cc_start: 0.8276 (t0) cc_final: 0.8008 (t0) REVERT: E 90 MET cc_start: 0.7278 (tpp) cc_final: 0.6947 (mpp) REVERT: E 131 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: F 84 MET cc_start: 0.7216 (mmm) cc_final: 0.6910 (mmm) REVERT: G 62 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7364 (tt) REVERT: G 74 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8408 (mtpp) REVERT: W 278 MET cc_start: 0.5150 (mmm) cc_final: 0.4607 (mmm) REVERT: W 320 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6249 (mt) REVERT: W 323 LYS cc_start: 0.7617 (tttt) cc_final: 0.7166 (ptmt) REVERT: W 412 LYS cc_start: 0.6699 (tttm) cc_final: 0.6382 (ttpt) REVERT: W 413 TRP cc_start: 0.7822 (m-90) cc_final: 0.6124 (m-90) REVERT: W 432 LYS cc_start: 0.7412 (tptt) cc_final: 0.6679 (ttpt) REVERT: W 477 GLU cc_start: 0.7612 (mp0) cc_final: 0.7357 (mp0) REVERT: W 482 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7312 (mmt-90) REVERT: W 485 GLN cc_start: 0.7956 (mp10) cc_final: 0.7674 (mp10) REVERT: W 507 GLU cc_start: 0.7107 (tt0) cc_final: 0.6383 (tt0) REVERT: W 545 TRP cc_start: 0.8396 (m100) cc_final: 0.8104 (m100) REVERT: W 547 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7713 (ttp-110) REVERT: W 568 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: W 570 MET cc_start: 0.7494 (tpp) cc_final: 0.7231 (mpp) REVERT: W 598 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7954 (ttmm) REVERT: W 599 ASP cc_start: 0.7826 (m-30) cc_final: 0.7399 (m-30) REVERT: W 614 ASP cc_start: 0.8058 (t0) cc_final: 0.7780 (t0) REVERT: W 629 THR cc_start: 0.8256 (t) cc_final: 0.7989 (m) REVERT: W 754 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7635 (mm-30) REVERT: W 963 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7395 (mt-10) REVERT: W 1056 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6934 (mm-30) REVERT: W 1058 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6646 (tm-30) REVERT: W 1059 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: W 1060 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.6777 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7215 (mm-30) REVERT: W 1065 GLU cc_start: 0.7269 (pp20) cc_final: 0.6493 (pp20) outliers start: 32 outliers final: 18 residues processed: 219 average time/residue: 0.4105 time to fit residues: 124.3687 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 : 1.440 ------------------------------------------------------------------------------- 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 111 ILE 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 62 ILE 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 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 690 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 151 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 25 optimal weight: 0.0170 chunk 161 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 114 optimal weight: 0.0670 chunk 112 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 133 optimal weight: 0.0070 overall best weight: 0.4174 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.179100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136674 restraints weight = 27449.473| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.67 r_work: 0.3530 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.6586 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= 0.134 Angle : 0.534 10.124 27619 Z= 0.307 Chirality : 0.035 0.181 3067 Planarity : 0.004 0.060 2430 Dihedral : 28.368 175.636 5062 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 16.93 % Favored : 81.20 % 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: 1.32 (0.23), residues: 1462 helix: 2.06 (0.18), residues: 835 sheet: -0.25 (0.75), residues: 56 loop : -0.83 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 491 HIS 0.005 0.001 HIS W 675 PHE 0.019 0.001 PHE W 748 TYR 0.023 0.001 TYR W 484 ARG 0.010 0.000 ARG W1052 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 902) hydrogen bonds : angle 3.19925 ( 2362) covalent geometry : bond 0.00290 (19485) covalent geometry : angle 0.53421 (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 230 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7732 (mtm-85) REVERT: B 84 MET cc_start: 0.7908 (mmm) cc_final: 0.7494 (mmm) REVERT: C 29 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6972 (ttp-170) REVERT: D 56 MET cc_start: 0.7796 (mmm) cc_final: 0.7501 (tpp) REVERT: D 90 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: D 120 SER cc_start: 0.8771 (m) cc_final: 0.8235 (p) REVERT: E 77 ASP cc_start: 0.8274 (t0) cc_final: 0.8016 (t0) REVERT: E 90 MET cc_start: 0.7253 (tpp) cc_final: 0.6876 (mpp) REVERT: F 84 MET cc_start: 0.7177 (mmm) cc_final: 0.6834 (mmm) REVERT: G 65 LEU cc_start: 0.8005 (mt) cc_final: 0.7652 (mp) REVERT: G 74 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8418 (mtpp) REVERT: W 278 MET cc_start: 0.5130 (mmm) cc_final: 0.4603 (mmm) REVERT: W 279 ASP cc_start: 0.4114 (t0) cc_final: 0.3043 (t0) REVERT: W 320 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6100 (mt) REVERT: W 323 LYS cc_start: 0.7614 (tttt) cc_final: 0.7150 (ptmt) REVERT: W 378 GLN cc_start: 0.8450 (mp10) cc_final: 0.8167 (pm20) REVERT: W 412 LYS cc_start: 0.6557 (tttm) cc_final: 0.6263 (ttpt) REVERT: W 413 TRP cc_start: 0.7757 (m-90) cc_final: 0.5979 (m-90) REVERT: W 432 LYS cc_start: 0.7389 (tptt) cc_final: 0.6657 (ttpt) REVERT: W 477 GLU cc_start: 0.7582 (mp0) cc_final: 0.7321 (mp0) REVERT: W 485 GLN cc_start: 0.7974 (mp10) cc_final: 0.7581 (mp10) REVERT: W 507 GLU cc_start: 0.7141 (tt0) cc_final: 0.6472 (tt0) REVERT: W 527 HIS cc_start: 0.7664 (m-70) cc_final: 0.7114 (m-70) REVERT: W 545 TRP cc_start: 0.8327 (m100) cc_final: 0.7950 (m100) REVERT: W 547 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7636 (ttp-110) REVERT: W 568 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: W 587 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7132 (p0) REVERT: W 598 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7924 (ttmm) REVERT: W 599 ASP cc_start: 0.7823 (m-30) cc_final: 0.7463 (m-30) REVERT: W 614 ASP cc_start: 0.8065 (t0) cc_final: 0.7762 (t0) REVERT: W 629 THR cc_start: 0.8219 (t) cc_final: 0.7956 (m) REVERT: W 693 PHE cc_start: 0.6820 (m-80) cc_final: 0.6358 (m-80) REVERT: W 754 GLU cc_start: 0.7877 (mm-30) cc_final: 0.6853 (mm-30) REVERT: W 757 LYS cc_start: 0.8066 (mttt) cc_final: 0.7208 (mttt) REVERT: W 766 LYS cc_start: 0.6392 (pttt) cc_final: 0.6045 (pttm) REVERT: W 963 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7267 (pt0) REVERT: W 1053 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7032 (mpp-170) REVERT: W 1056 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6939 (mm-30) REVERT: W 1058 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6709 (tm-30) REVERT: W 1059 GLU cc_start: 0.7906 (tp30) cc_final: 0.7407 (mp0) REVERT: W 1060 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.6750 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7152 (mm-30) REVERT: W 1065 GLU cc_start: 0.7307 (pp20) cc_final: 0.6528 (pp20) outliers start: 24 outliers final: 17 residues processed: 222 average time/residue: 0.4014 time to fit residues: 123.3753 Evaluate side-chains 224 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 111 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU 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 441 PHE Chi-restraints excluded: chain W residue 476 HIS Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 543 THR Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 587 ASN Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 661 MET Chi-restraints excluded: chain W residue 690 LEU Chi-restraints excluded: chain W residue 914 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** E 108 ASN G 73 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 GLN ** W 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.175184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132344 restraints weight = 27331.418| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.65 r_work: 0.3471 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19485 Z= 0.191 Angle : 0.574 9.430 27619 Z= 0.329 Chirality : 0.038 0.260 3067 Planarity : 0.004 0.067 2430 Dihedral : 28.527 175.006 5062 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 17.47 % Favored : 80.73 % 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: 1.07 (0.23), residues: 1462 helix: 1.84 (0.18), residues: 834 sheet: -0.27 (0.75), residues: 56 loop : -0.90 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 491 HIS 0.007 0.001 HIS W 675 PHE 0.019 0.001 PHE W 748 TYR 0.024 0.001 TYR W 484 ARG 0.008 0.000 ARG W1053 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 902) hydrogen bonds : angle 3.34112 ( 2362) covalent geometry : bond 0.00431 (19485) covalent geometry : angle 0.57442 (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 217 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.487 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: 0.7911 (mmm) cc_final: 0.7411 (mmm) REVERT: C 29 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: C 88 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8627 (mmt180) REVERT: D 56 MET cc_start: 0.7821 (mmm) cc_final: 0.7620 (tpp) REVERT: D 90 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: D 120 SER cc_start: 0.8817 (m) cc_final: 0.8323 (p) REVERT: E 77 ASP cc_start: 0.8279 (t0) cc_final: 0.8016 (t0) REVERT: E 90 MET cc_start: 0.7303 (tpp) cc_final: 0.6994 (mpp) REVERT: F 84 MET cc_start: 0.7244 (mmm) cc_final: 0.6935 (mmm) REVERT: W 278 MET cc_start: 0.5164 (mmm) cc_final: 0.4633 (mmm) REVERT: W 279 ASP cc_start: 0.4874 (t0) cc_final: 0.3860 (t0) REVERT: W 320 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6234 (mt) REVERT: W 323 LYS cc_start: 0.7647 (tttt) cc_final: 0.7216 (ptmt) REVERT: W 339 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7752 (pttm) REVERT: W 412 LYS cc_start: 0.6582 (tttm) cc_final: 0.6323 (ttpt) REVERT: W 413 TRP cc_start: 0.7771 (m-90) cc_final: 0.5946 (m-90) REVERT: W 432 LYS cc_start: 0.7400 (tptt) cc_final: 0.6647 (tmmt) REVERT: W 485 GLN cc_start: 0.7927 (mp10) cc_final: 0.7436 (mp10) REVERT: W 507 GLU cc_start: 0.7173 (tt0) cc_final: 0.6516 (tt0) REVERT: W 527 HIS cc_start: 0.7649 (m-70) cc_final: 0.7373 (m170) REVERT: W 547 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7660 (ttp-110) REVERT: W 568 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7810 (mtm-85) REVERT: W 587 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7205 (p0) REVERT: W 598 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7822 (ttmm) REVERT: W 599 ASP cc_start: 0.7819 (m-30) cc_final: 0.7394 (m-30) REVERT: W 614 ASP cc_start: 0.8048 (t0) cc_final: 0.7762 (t0) REVERT: W 629 THR cc_start: 0.8276 (t) cc_final: 0.8007 (m) REVERT: W 754 GLU cc_start: 0.7926 (mm-30) cc_final: 0.6764 (mm-30) REVERT: W 757 LYS cc_start: 0.8162 (mttt) cc_final: 0.7250 (mttt) REVERT: W 766 LYS cc_start: 0.6497 (pttt) cc_final: 0.6116 (pttm) REVERT: W 963 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7449 (mt-10) REVERT: W 1056 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7079 (mm-30) REVERT: W 1059 GLU cc_start: 0.8008 (tp30) cc_final: 0.7486 (mp0) REVERT: W 1060 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.6949 (tpp-160) REVERT: W 1063 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7092 (mm-30) outliers start: 23 outliers final: 16 residues processed: 209 average time/residue: 0.4116 time to fit residues: 119.0803 Evaluate side-chains 213 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 90 GLU 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 339 LYS Chi-restraints excluded: chain W residue 437 ILE 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 543 THR Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 587 ASN Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 690 LEU Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 990 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 161 optimal weight: 0.0470 chunk 169 optimal weight: 0.0980 chunk 143 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 168 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.2016 ------------------------------------------------------------------------------- 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 341 GLN ** W 525 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 = 0.4208 r_free = 0.4208 target = 0.181132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139381 restraints weight = 27472.805| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.65 r_work: 0.3562 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.6884 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= 0.129 Angle : 0.538 10.277 27619 Z= 0.308 Chirality : 0.034 0.187 3067 Planarity : 0.004 0.103 2430 Dihedral : 28.282 176.784 5062 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.56 % Allowed : 17.63 % Favored : 80.81 % 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: 1.34 (0.23), residues: 1462 helix: 2.08 (0.18), residues: 836 sheet: -0.14 (0.75), residues: 56 loop : -0.83 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP W 491 HIS 0.006 0.001 HIS B 75 PHE 0.019 0.001 PHE W 748 TYR 0.024 0.001 TYR W 484 ARG 0.008 0.000 ARG W 482 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 902) hydrogen bonds : angle 3.19018 ( 2362) covalent geometry : bond 0.00273 (19485) covalent geometry : angle 0.53830 (27619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10715.44 seconds wall clock time: 185 minutes 1.38 seconds (11101.38 seconds total)