Starting phenix.real_space_refine on Sat Jul 4 03:40:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_49406.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_49406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_49406.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_49406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nh8_49406/07_2026/9nh8_49406.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.93, per 1000 atoms: 0.16 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: 1.35 Conformation dependent library (CDL) restraints added in 373.9 milliseconds 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: 2.21 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: 3.42 Time building geometry restraints manager: 1.84 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=" C1' DT I 14 " pdb=" N1 DT I 14 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.63e+01 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=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.44e+01 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 26906 2.37 - 4.74: 656 4.74 - 7.12: 39 7.12 - 9.49: 13 9.49 - 11.86: 5 Bond angle restraints: 27619 Sorted by residual: angle pdb=" O4' DG I -58 " pdb=" C4' DG I -58 " pdb=" C3' DG I -58 " ideal model delta sigma weight residual 106.00 102.68 3.32 6.00e-01 2.78e+00 3.06e+01 angle pdb=" O4' DC J -9 " pdb=" C4' DC J -9 " pdb=" C3' DC J -9 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.94e+01 angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" O5' DG I 47 " pdb=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 109.40 113.49 -4.09 8.00e-01 1.56e+00 2.61e+01 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 ... (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 - 0.080: 2753 0.080 - 0.161: 301 0.161 - 0.241: 8 0.241 - 0.321: 2 0.321 - 0.402: 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 2.34 -2.74 -0.40 2.00e-01 2.50e+01 4.03e+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 2.34 -2.72 -0.39 2.00e-01 2.50e+01 3.72e+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 2.34 -2.69 -0.36 2.00e-01 2.50e+01 3.16e+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: 1.630 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.007 0.306 19485 Z= 0.527 Angle : 0.858 11.861 27619 Z= 0.668 Chirality : 0.050 0.402 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.011 0.001 ARG W 443 TYR 0.023 0.002 TYR B 98 PHE 0.019 0.002 PHE W 882 TRP 0.042 0.003 TRP W 413 HIS 0.027 0.002 HIS W 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.53 (19485) covalent geometry : angle 0.85767 / 0.67 (27619) hydrogen bonds : bond 0.18513 / 12.35 ( 902) hydrogen bonds : angle 6.19756 / 4.39 ( 2362) *********************** 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 : 0.371 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: 0.1416 time to fit residues: 50.4091 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 : 0.455 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN H 44 GLN H 60 ASN W 340 GLN W 445 GLN ** W 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 587 ASN W 658 HIS W1061 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.175720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132910 restraints weight = 27837.305| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.80 r_work: 0.3475 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 19485 Z= 0.392 Angle : 0.949 10.499 27619 Z= 0.514 Chirality : 0.062 0.371 3067 Planarity : 0.007 0.066 2430 Dihedral : 29.314 170.541 5081 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % Rotamer: Outliers : 2.65 % Allowed : 12.40 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1462 helix: -0.12 (0.17), residues: 819 sheet: -1.11 (0.68), residues: 62 loop : -1.38 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 45 TYR 0.030 0.003 TYR F 98 PHE 0.022 0.003 PHE W 748 TRP 0.060 0.004 TRP W 491 HIS 0.014 0.003 HIS W 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.39 (19485) covalent geometry : angle 0.94946 / 0.51 (27619) hydrogen bonds : bond 0.07228 / 4.85 ( 902) hydrogen bonds : angle 4.52576 / 3.25 ( 2362) *********************** 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 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7707 (mp) REVERT: B 36 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7648 (mtt180) REVERT: B 84 MET cc_start: 0.7972 (mmm) cc_final: 0.7593 (mmm) REVERT: E 77 ASP cc_start: 0.8163 (t0) cc_final: 0.7839 (t0) REVERT: E 96 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7921 (m) REVERT: F 84 MET cc_start: 0.7505 (mmm) cc_final: 0.7090 (mmm) REVERT: G 36 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8371 (mtmm) REVERT: W 275 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6380 (tp30) REVERT: W 278 MET cc_start: 0.4480 (mmm) cc_final: 0.4207 (mmm) REVERT: W 323 LYS cc_start: 0.7140 (tttt) cc_final: 0.6807 (ttpt) REVERT: W 386 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8098 (mtmt) REVERT: W 412 LYS cc_start: 0.7063 (tttm) cc_final: 0.6282 (mtpp) REVERT: W 514 ILE cc_start: 0.6998 (tp) cc_final: 0.6768 (mm) REVERT: W 527 HIS cc_start: 0.7674 (m-70) cc_final: 0.7114 (m170) REVERT: W 546 GLN cc_start: 0.8479 (tt0) cc_final: 0.7115 (tt0) REVERT: W 568 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7404 (mtm-85) REVERT: W 570 MET cc_start: 0.7624 (tpp) cc_final: 0.7283 (mpp) REVERT: W 615 GLU cc_start: 0.7818 (mp0) cc_final: 0.7498 (mp0) REVERT: W 627 TYR cc_start: 0.8308 (t80) cc_final: 0.7386 (t80) REVERT: W 629 THR cc_start: 0.8332 (t) cc_final: 0.7971 (m) REVERT: W 652 GLU cc_start: 0.7647 (tt0) cc_final: 0.7273 (tt0) REVERT: W 1061 GLN cc_start: 0.7451 (tm130) cc_final: 0.7249 (tm-30) REVERT: W 1065 GLU cc_start: 0.6987 (pp20) cc_final: 0.6751 (pp20) outliers start: 34 outliers final: 13 residues processed: 223 average time/residue: 0.1370 time to fit residues: 44.1379 Evaluate side-chains 211 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain W residue 275 GLU Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 395 ILE Chi-restraints excluded: chain W residue 441 PHE 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 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 106 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN H 60 ASN W 304 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 GLN W 515 GLN ** W 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 636 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.136383 restraints weight = 28052.621| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.72 r_work: 0.3517 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19485 Z= 0.170 Angle : 0.664 10.109 27619 Z= 0.382 Chirality : 0.046 0.254 3067 Planarity : 0.004 0.047 2430 Dihedral : 29.197 171.104 5064 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 15.05 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1462 helix: 0.70 (0.18), residues: 837 sheet: -0.57 (0.77), residues: 54 loop : -1.26 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.014 0.001 TYR F 98 PHE 0.016 0.001 PHE W 748 TRP 0.041 0.002 TRP W 491 HIS 0.007 0.001 HIS W 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (19485) covalent geometry : angle 0.66410 / 0.38 (27619) hydrogen bonds : bond 0.05281 / 3.48 ( 902) hydrogen bonds : angle 3.96854 / 2.85 ( 2362) *********************** 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 213 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7834 (ttm170) REVERT: A 109 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7693 (mp) REVERT: C 29 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6731 (ttp-110) REVERT: C 95 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8423 (ttmm) REVERT: E 77 ASP cc_start: 0.8179 (t0) cc_final: 0.7890 (t0) REVERT: F 84 MET cc_start: 0.7358 (mmm) cc_final: 0.6950 (mmm) REVERT: G 36 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8219 (mmmm) REVERT: G 74 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8285 (mtpp) REVERT: W 276 ARG cc_start: 0.6385 (ttt180) cc_final: 0.5694 (ttt90) REVERT: W 278 MET cc_start: 0.4313 (mmm) cc_final: 0.4098 (mmm) REVERT: W 320 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6836 (mt) REVERT: W 323 LYS cc_start: 0.7028 (tttt) cc_final: 0.6574 (ptmt) REVERT: W 386 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8031 (mtmt) REVERT: W 412 LYS cc_start: 0.6831 (tttm) cc_final: 0.6010 (mtpp) REVERT: W 514 ILE cc_start: 0.6966 (tp) cc_final: 0.6691 (mm) REVERT: W 527 HIS cc_start: 0.7707 (m-70) cc_final: 0.7422 (m170) REVERT: W 546 GLN cc_start: 0.8364 (tt0) cc_final: 0.7298 (tt0) REVERT: W 570 MET cc_start: 0.7525 (tpp) cc_final: 0.7196 (mpp) REVERT: W 599 ASP cc_start: 0.7756 (m-30) cc_final: 0.7409 (m-30) REVERT: W 614 ASP cc_start: 0.7747 (t0) cc_final: 0.7543 (t0) REVERT: W 627 TYR cc_start: 0.8257 (t80) cc_final: 0.7387 (t80) REVERT: W 629 THR cc_start: 0.8282 (t) cc_final: 0.7970 (m) REVERT: W 652 GLU cc_start: 0.7512 (tt0) cc_final: 0.7178 (tt0) REVERT: W 661 MET cc_start: 0.7602 (mtt) cc_final: 0.7322 (mtt) REVERT: W 690 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7451 (pp) REVERT: W 757 LYS cc_start: 0.8066 (mttt) cc_final: 0.7633 (mttt) REVERT: W 766 LYS cc_start: 0.5880 (pttt) cc_final: 0.5625 (ptpp) REVERT: W 914 THR cc_start: 0.4725 (OUTLIER) cc_final: 0.3980 (p) REVERT: W 921 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: W 924 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7543 (mm-30) REVERT: W 964 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7264 (tm-30) outliers start: 21 outliers final: 8 residues processed: 205 average time/residue: 0.1492 time to fit residues: 43.6173 Evaluate side-chains 198 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN 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 W residue 304 ASN Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 395 ILE Chi-restraints excluded: chain W residue 441 PHE 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 690 LEU Chi-restraints excluded: chain W residue 755 LEU Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 921 ASP 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 150 optimal weight: 8.9990 chunk 124 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 157 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 138 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 327 HIS W 341 GLN ** W 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 587 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.178530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135894 restraints weight = 28182.266| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.75 r_work: 0.3515 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19485 Z= 0.146 Angle : 0.620 8.192 27619 Z= 0.358 Chirality : 0.044 0.252 3067 Planarity : 0.004 0.042 2430 Dihedral : 29.090 171.248 5064 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.87 % Allowed : 14.82 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.22), residues: 1462 helix: 1.17 (0.18), residues: 843 sheet: -0.53 (0.76), residues: 54 loop : -1.18 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.011 0.001 TYR W 561 PHE 0.016 0.001 PHE W 748 TRP 0.024 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (19485) covalent geometry : angle 0.62002 / 0.36 (27619) hydrogen bonds : bond 0.04620 / 3.07 ( 902) hydrogen bonds : angle 3.76388 / 2.70 ( 2362) *********************** 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 212 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.7845 (mmp) cc_final: 0.7441 (mmt) REVERT: C 29 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6806 (ttp-110) REVERT: E 77 ASP cc_start: 0.8218 (t0) cc_final: 0.7946 (t0) REVERT: E 90 MET cc_start: 0.7376 (tpp) cc_final: 0.6771 (mpp) REVERT: G 36 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8259 (mmmm) REVERT: G 74 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8313 (mtpp) REVERT: W 276 ARG cc_start: 0.6344 (ttt180) cc_final: 0.5592 (ttt90) REVERT: W 278 MET cc_start: 0.4442 (mmm) cc_final: 0.4147 (mmm) REVERT: W 320 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6757 (mt) REVERT: W 323 LYS cc_start: 0.7104 (tttt) cc_final: 0.6643 (ptmt) REVERT: W 386 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8124 (mtmt) REVERT: W 393 ARG cc_start: 0.7513 (ptp90) cc_final: 0.7235 (ttp-110) REVERT: W 412 LYS cc_start: 0.6761 (tttm) cc_final: 0.6427 (ttpt) REVERT: W 514 ILE cc_start: 0.6920 (tp) cc_final: 0.6702 (mm) REVERT: W 546 GLN cc_start: 0.8325 (tt0) cc_final: 0.7416 (tt0) REVERT: W 568 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7727 (mtm-85) REVERT: W 570 MET cc_start: 0.7561 (tpp) cc_final: 0.7210 (mpp) REVERT: W 589 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.5875 (tt) REVERT: W 599 ASP cc_start: 0.7813 (m-30) cc_final: 0.7505 (m-30) REVERT: W 614 ASP cc_start: 0.7811 (t0) cc_final: 0.7592 (t0) REVERT: W 627 TYR cc_start: 0.8261 (t80) cc_final: 0.7367 (t80) REVERT: W 629 THR cc_start: 0.8266 (t) cc_final: 0.7958 (m) REVERT: W 652 GLU cc_start: 0.7471 (tt0) cc_final: 0.7123 (tt0) REVERT: W 661 MET cc_start: 0.7637 (mtt) cc_final: 0.7386 (mtt) REVERT: W 690 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7472 (pp) REVERT: W 757 LYS cc_start: 0.8062 (mttt) cc_final: 0.7616 (mttt) REVERT: W 914 THR cc_start: 0.4747 (OUTLIER) cc_final: 0.4019 (p) REVERT: W 924 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7477 (mm-30) REVERT: W 964 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: W 1065 GLU cc_start: 0.7026 (pp20) cc_final: 0.6499 (pp20) outliers start: 24 outliers final: 10 residues processed: 203 average time/residue: 0.1491 time to fit residues: 43.2377 Evaluate side-chains 200 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 690 LEU 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 36 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 142 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 GLN W 434 GLN ** W 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 587 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.172350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129431 restraints weight = 27768.160| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.72 r_work: 0.3431 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19485 Z= 0.241 Angle : 0.716 8.935 27619 Z= 0.399 Chirality : 0.049 0.284 3067 Planarity : 0.005 0.049 2430 Dihedral : 29.216 174.712 5062 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.96 % Allowed : 14.59 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1462 helix: 1.22 (0.18), residues: 823 sheet: -0.79 (0.71), residues: 62 loop : -1.12 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 572 TYR 0.020 0.002 TYR A 99 PHE 0.015 0.002 PHE W 277 TRP 0.041 0.002 TRP W 332 HIS 0.014 0.002 HIS W 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (19485) covalent geometry : angle 0.71630 / 0.40 (27619) hydrogen bonds : bond 0.05741 / 3.90 ( 902) hydrogen bonds : angle 3.90375 / 2.79 ( 2362) *********************** 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 233 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.320 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 109 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 115 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7956 (mtmm) REVERT: C 29 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6853 (ttp-170) REVERT: E 77 ASP cc_start: 0.8304 (t0) cc_final: 0.7996 (t0) REVERT: E 90 MET cc_start: 0.7333 (tpp) cc_final: 0.6981 (mpp) REVERT: E 131 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: F 84 MET cc_start: 0.7384 (mmm) cc_final: 0.6973 (mmm) REVERT: G 36 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8342 (mmmm) REVERT: G 74 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8360 (mtpp) REVERT: W 278 MET cc_start: 0.4728 (mmm) cc_final: 0.4292 (mmm) REVERT: W 320 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6681 (mt) REVERT: W 323 LYS cc_start: 0.7437 (tttt) cc_final: 0.7039 (ptmt) REVERT: W 386 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8278 (mtmt) REVERT: W 393 ARG cc_start: 0.7660 (ptp90) cc_final: 0.7322 (ttp-110) REVERT: W 412 LYS cc_start: 0.6735 (tttm) cc_final: 0.6384 (ttpt) REVERT: W 507 GLU cc_start: 0.7015 (tt0) cc_final: 0.6260 (tt0) REVERT: W 546 GLN cc_start: 0.8371 (tt0) cc_final: 0.7454 (tt0) REVERT: W 568 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.6911 (mpp80) REVERT: W 570 MET cc_start: 0.7504 (tpp) cc_final: 0.7144 (mpp) REVERT: W 589 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.6296 (tt) REVERT: W 598 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7940 (ttmm) REVERT: W 599 ASP cc_start: 0.7811 (m-30) cc_final: 0.7547 (m-30) REVERT: W 614 ASP cc_start: 0.7948 (t0) cc_final: 0.7693 (t0) REVERT: W 629 THR cc_start: 0.8273 (t) cc_final: 0.7996 (m) REVERT: W 652 GLU cc_start: 0.7551 (tt0) cc_final: 0.7231 (pt0) REVERT: W 695 LEU cc_start: 0.7281 (mt) cc_final: 0.6707 (mp) REVERT: W 757 LYS cc_start: 0.8064 (mttt) cc_final: 0.7593 (mttt) REVERT: W 766 LYS cc_start: 0.6198 (pttt) cc_final: 0.5841 (ptpp) REVERT: W 914 THR cc_start: 0.5224 (OUTLIER) cc_final: 0.4451 (p) REVERT: W 924 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7578 (mt-10) REVERT: W 964 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: W 1050 ASP cc_start: 0.7511 (p0) cc_final: 0.6891 (t0) REVERT: W 1065 GLU cc_start: 0.7152 (pp20) cc_final: 0.6592 (pp20) outliers start: 38 outliers final: 16 residues processed: 218 average time/residue: 0.1518 time to fit residues: 47.0094 Evaluate side-chains 213 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain W residue 316 ILE Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 409 TYR Chi-restraints excluded: chain W residue 438 ASP Chi-restraints excluded: chain W residue 441 PHE 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 589 LEU Chi-restraints excluded: chain W residue 590 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 755 LEU Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Chi-restraints excluded: chain W residue 1062 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 158 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 GLN ** W 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.174235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131447 restraints weight = 27672.211| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.69 r_work: 0.3470 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19485 Z= 0.147 Angle : 0.623 11.902 27619 Z= 0.356 Chirality : 0.044 0.255 3067 Planarity : 0.004 0.042 2430 Dihedral : 29.079 175.955 5062 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.03 % Allowed : 15.60 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1462 helix: 1.46 (0.18), residues: 835 sheet: -0.72 (0.71), residues: 62 loop : -1.14 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.011 0.001 TYR F 98 PHE 0.014 0.001 PHE W 277 TRP 0.015 0.001 TRP W 332 HIS 0.007 0.001 HIS W 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (19485) covalent geometry : angle 0.62271 / 0.36 (27619) hydrogen bonds : bond 0.04551 / 3.01 ( 902) hydrogen bonds : angle 3.64949 / 2.62 ( 2362) *********************** 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 210 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.389 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 115 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7833 (mtmm) REVERT: B 84 MET cc_start: 0.7913 (mmt) cc_final: 0.7706 (mmt) REVERT: C 29 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6874 (ttp-170) REVERT: D 56 MET cc_start: 0.7887 (mmm) cc_final: 0.7591 (tpp) REVERT: E 77 ASP cc_start: 0.8301 (t0) cc_final: 0.7990 (t0) REVERT: E 90 MET cc_start: 0.7257 (tpp) cc_final: 0.6877 (mpp) REVERT: F 84 MET cc_start: 0.7329 (mmm) cc_final: 0.6983 (mmm) REVERT: G 36 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8353 (mmmm) REVERT: G 62 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7341 (tt) REVERT: H 56 MET cc_start: 0.7728 (tpp) cc_final: 0.7518 (tpp) REVERT: W 275 GLU cc_start: 0.6257 (tp30) cc_final: 0.5764 (tp30) REVERT: W 276 ARG cc_start: 0.6386 (ttt180) cc_final: 0.5233 (ttt90) REVERT: W 278 MET cc_start: 0.4149 (mmm) cc_final: 0.3817 (mmm) REVERT: W 320 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6543 (mt) REVERT: W 323 LYS cc_start: 0.7310 (tttt) cc_final: 0.6449 (ptmt) REVERT: W 386 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8192 (mtmt) REVERT: W 393 ARG cc_start: 0.7648 (ptp90) cc_final: 0.7300 (ttp-110) REVERT: W 410 TYR cc_start: 0.5216 (OUTLIER) cc_final: 0.4957 (t80) REVERT: W 412 LYS cc_start: 0.6608 (tttm) cc_final: 0.6348 (ttpt) REVERT: W 448 THR cc_start: 0.8027 (p) cc_final: 0.7824 (p) REVERT: W 477 GLU cc_start: 0.7582 (mp0) cc_final: 0.7291 (mp0) REVERT: W 507 GLU cc_start: 0.6994 (tt0) cc_final: 0.6235 (tt0) REVERT: W 546 GLN cc_start: 0.8309 (tt0) cc_final: 0.7671 (tt0) REVERT: W 568 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: W 570 MET cc_start: 0.7430 (tpp) cc_final: 0.7010 (mpp) REVERT: W 589 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.6020 (tt) REVERT: W 599 ASP cc_start: 0.7751 (m-30) cc_final: 0.7203 (m-30) REVERT: W 614 ASP cc_start: 0.7907 (t0) cc_final: 0.7645 (t0) REVERT: W 629 THR cc_start: 0.8183 (t) cc_final: 0.7905 (m) REVERT: W 652 GLU cc_start: 0.7455 (tt0) cc_final: 0.7234 (pt0) REVERT: W 695 LEU cc_start: 0.6976 (mt) cc_final: 0.6213 (tp) REVERT: W 757 LYS cc_start: 0.8073 (mttt) cc_final: 0.7625 (mttt) REVERT: W 766 LYS cc_start: 0.6202 (pttt) cc_final: 0.5942 (ptpp) REVERT: W 914 THR cc_start: 0.5239 (OUTLIER) cc_final: 0.4631 (p) REVERT: W 920 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6306 (pm20) REVERT: W 924 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7633 (mt-10) REVERT: W 964 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: W 1065 GLU cc_start: 0.7158 (pp20) cc_final: 0.6528 (pp20) outliers start: 26 outliers final: 12 residues processed: 200 average time/residue: 0.1582 time to fit residues: 44.6319 Evaluate side-chains 204 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS 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 F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 410 TYR Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 755 LEU Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Chi-restraints excluded: chain W residue 1053 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN H 60 ASN W 304 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 341 GLN W 434 GLN ** W 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W1061 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.170237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127166 restraints weight = 27732.741| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.74 r_work: 0.3409 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19485 Z= 0.276 Angle : 0.717 9.242 27619 Z= 0.396 Chirality : 0.049 0.301 3067 Planarity : 0.005 0.043 2430 Dihedral : 29.208 178.623 5062 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.50 % Allowed : 15.37 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1462 helix: 1.17 (0.18), residues: 832 sheet: -0.75 (0.72), residues: 62 loop : -1.24 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 697 TYR 0.032 0.002 TYR W 374 PHE 0.018 0.002 PHE H 67 TRP 0.012 0.002 TRP W 576 HIS 0.010 0.002 HIS W 761 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.28 (19485) covalent geometry : angle 0.71679 / 0.40 (27619) hydrogen bonds : bond 0.05583 / 3.78 ( 902) hydrogen bonds : angle 3.84462 / 2.75 ( 2362) *********************** 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 226 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.528 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 109 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7598 (mp) REVERT: A 115 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: B 36 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7794 (mtt90) REVERT: C 29 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.6963 (ttp-170) REVERT: C 88 ARG cc_start: 0.8864 (mmt-90) cc_final: 0.8630 (mmt180) REVERT: D 56 MET cc_start: 0.7977 (mmm) cc_final: 0.7394 (mmm) REVERT: D 98 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7932 (mp) REVERT: E 77 ASP cc_start: 0.8284 (t0) cc_final: 0.7971 (t0) REVERT: E 90 MET cc_start: 0.7246 (tpp) cc_final: 0.6958 (tpp) REVERT: E 131 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7749 (mtt180) REVERT: F 84 MET cc_start: 0.7444 (mmm) cc_final: 0.7028 (mmm) REVERT: G 36 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: W 275 GLU cc_start: 0.6222 (tp30) cc_final: 0.5710 (tp30) REVERT: W 278 MET cc_start: 0.4545 (mmm) cc_final: 0.4205 (mmm) REVERT: W 320 ILE cc_start: 0.7111 (OUTLIER) cc_final: 0.6716 (mt) REVERT: W 323 LYS cc_start: 0.7486 (tttt) cc_final: 0.6502 (ptmt) REVERT: W 386 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8271 (mtmt) REVERT: W 412 LYS cc_start: 0.6648 (tttm) cc_final: 0.6360 (ttpt) REVERT: W 477 GLU cc_start: 0.7548 (mp0) cc_final: 0.7312 (mp0) REVERT: W 507 GLU cc_start: 0.6939 (tt0) cc_final: 0.6258 (tt0) REVERT: W 527 HIS cc_start: 0.7697 (m-70) cc_final: 0.7055 (m170) REVERT: W 542 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (tp) REVERT: W 556 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7514 (mmm) REVERT: W 568 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.6756 (mpp80) REVERT: W 570 MET cc_start: 0.7480 (tpp) cc_final: 0.7030 (mpp) REVERT: W 589 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.6135 (tt) REVERT: W 599 ASP cc_start: 0.7798 (m-30) cc_final: 0.7481 (m-30) REVERT: W 614 ASP cc_start: 0.7987 (t0) cc_final: 0.7699 (t0) REVERT: W 629 THR cc_start: 0.8193 (t) cc_final: 0.7933 (m) REVERT: W 652 GLU cc_start: 0.7532 (tt0) cc_final: 0.7182 (tt0) REVERT: W 695 LEU cc_start: 0.7118 (mt) cc_final: 0.6646 (tp) REVERT: W 754 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7149 (mm-30) REVERT: W 757 LYS cc_start: 0.8087 (mttt) cc_final: 0.7389 (mttt) REVERT: W 761 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5967 (t-90) REVERT: W 766 LYS cc_start: 0.6337 (pttt) cc_final: 0.5979 (ptpp) REVERT: W 920 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6443 (pm20) REVERT: W 924 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7513 (mt-10) REVERT: W 964 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: W 1060 ARG cc_start: 0.7376 (tpp-160) cc_final: 0.6439 (tpp-160) REVERT: W 1069 MET cc_start: 0.6836 (mmm) cc_final: 0.6584 (mmm) outliers start: 32 outliers final: 17 residues processed: 214 average time/residue: 0.1735 time to fit residues: 52.0155 Evaluate side-chains 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS 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 98 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 441 PHE Chi-restraints excluded: chain W residue 486 LEU Chi-restraints excluded: chain W residue 530 TYR Chi-restraints excluded: chain W residue 542 LEU Chi-restraints excluded: chain W residue 556 MET Chi-restraints excluded: chain W residue 560 VAL Chi-restraints excluded: chain W residue 562 LEU Chi-restraints excluded: chain W residue 589 LEU Chi-restraints excluded: chain W residue 590 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 702 VAL 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 1053 ARG Chi-restraints excluded: chain W residue 1061 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 434 GLN W 445 GLN ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.172688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130054 restraints weight = 27443.790| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.68 r_work: 0.3445 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19485 Z= 0.153 Angle : 0.632 9.322 27619 Z= 0.360 Chirality : 0.044 0.259 3067 Planarity : 0.004 0.047 2430 Dihedral : 29.124 178.056 5062 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.42 % Allowed : 16.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.22), residues: 1462 helix: 1.42 (0.18), residues: 830 sheet: -0.36 (0.76), residues: 57 loop : -1.12 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 572 TYR 0.027 0.001 TYR W 374 PHE 0.013 0.001 PHE W 748 TRP 0.014 0.001 TRP W 491 HIS 0.005 0.001 HIS W 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (19485) covalent geometry : angle 0.63175 / 0.36 (27619) hydrogen bonds : bond 0.04598 / 3.04 ( 902) hydrogen bonds : angle 3.65638 / 2.62 ( 2362) *********************** 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 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.533 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 115 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: C 29 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.6928 (ttp-170) REVERT: D 56 MET cc_start: 0.7943 (mmm) cc_final: 0.7425 (mmm) REVERT: E 77 ASP cc_start: 0.8273 (t0) cc_final: 0.7965 (t0) REVERT: E 90 MET cc_start: 0.7212 (tpp) cc_final: 0.6911 (mpp) REVERT: F 84 MET cc_start: 0.7348 (mmm) cc_final: 0.7027 (mmm) REVERT: G 36 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8353 (mmmm) REVERT: G 62 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7356 (tt) REVERT: W 275 GLU cc_start: 0.6318 (tp30) cc_final: 0.5790 (tp30) REVERT: W 278 MET cc_start: 0.4421 (mmm) cc_final: 0.4055 (mmm) REVERT: W 320 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6586 (mt) REVERT: W 323 LYS cc_start: 0.7445 (tttt) cc_final: 0.6467 (ptmt) REVERT: W 386 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8293 (mtmt) REVERT: W 412 LYS cc_start: 0.6550 (tttm) cc_final: 0.6165 (ttpt) REVERT: W 477 GLU cc_start: 0.7540 (mp0) cc_final: 0.7284 (mp0) REVERT: W 507 GLU cc_start: 0.6896 (tt0) cc_final: 0.6155 (tt0) REVERT: W 513 THR cc_start: 0.7129 (p) cc_final: 0.6722 (t) REVERT: W 527 HIS cc_start: 0.7633 (m-70) cc_final: 0.6989 (m170) REVERT: W 568 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: W 570 MET cc_start: 0.7464 (tpp) cc_final: 0.7043 (mpp) REVERT: W 589 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.5990 (tt) REVERT: W 599 ASP cc_start: 0.7739 (m-30) cc_final: 0.7167 (m-30) REVERT: W 614 ASP cc_start: 0.7948 (t0) cc_final: 0.7680 (t0) REVERT: W 629 THR cc_start: 0.8146 (t) cc_final: 0.7885 (m) REVERT: W 754 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7103 (mm-30) REVERT: W 757 LYS cc_start: 0.8074 (mttt) cc_final: 0.7360 (mttt) REVERT: W 761 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.6115 (t-90) REVERT: W 766 LYS cc_start: 0.6300 (pttt) cc_final: 0.5947 (ptpp) REVERT: W 920 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6505 (pm20) REVERT: W 924 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7556 (mt-10) REVERT: W 964 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: W 1069 MET cc_start: 0.6875 (mmm) cc_final: 0.6652 (mmm) outliers start: 31 outliers final: 17 residues processed: 206 average time/residue: 0.1664 time to fit residues: 48.3422 Evaluate side-chains 214 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 115 LYS 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 F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 409 TYR 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 702 VAL 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 1053 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 105 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 162 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 32 optimal weight: 0.0370 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 340 GLN ** W 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126969 restraints weight = 27557.330| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.72 r_work: 0.3400 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19485 Z= 0.259 Angle : 0.703 11.614 27619 Z= 0.391 Chirality : 0.049 0.296 3067 Planarity : 0.005 0.049 2430 Dihedral : 29.194 179.400 5062 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 16.22 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1462 helix: 1.20 (0.18), residues: 829 sheet: -0.39 (0.77), residues: 57 loop : -1.17 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 71 TYR 0.024 0.002 TYR W 374 PHE 0.016 0.002 PHE D 67 TRP 0.023 0.002 TRP W 423 HIS 0.008 0.001 HIS W 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (19485) covalent geometry : angle 0.70298 / 0.39 (27619) hydrogen bonds : bond 0.05329 / 3.60 ( 902) hydrogen bonds : angle 3.76184 / 2.70 ( 2362) *********************** 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 218 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7670 (mp) REVERT: A 115 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8055 (mtmm) REVERT: B 36 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7819 (mtt90) REVERT: C 29 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7076 (ttp-170) REVERT: C 88 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8657 (mmt180) REVERT: D 56 MET cc_start: 0.7975 (mmm) cc_final: 0.7497 (mmm) REVERT: E 77 ASP cc_start: 0.8278 (t0) cc_final: 0.7966 (t0) REVERT: E 90 MET cc_start: 0.7275 (tpp) cc_final: 0.6986 (mpp) REVERT: F 84 MET cc_start: 0.7393 (mmm) cc_final: 0.7030 (mmm) REVERT: G 36 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8443 (mtpp) REVERT: G 73 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8185 (t0) REVERT: W 275 GLU cc_start: 0.6349 (tp30) cc_final: 0.5808 (tp30) REVERT: W 278 MET cc_start: 0.4551 (mmm) cc_final: 0.4155 (mmm) REVERT: W 320 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6689 (mt) REVERT: W 323 LYS cc_start: 0.7537 (tttt) cc_final: 0.6604 (ptmt) REVERT: W 386 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8328 (mtmt) REVERT: W 393 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7528 (ttp-110) REVERT: W 412 LYS cc_start: 0.6443 (tttm) cc_final: 0.6175 (ttpt) REVERT: W 432 LYS cc_start: 0.7617 (tptt) cc_final: 0.6795 (ttpt) REVERT: W 434 GLN cc_start: 0.6055 (tp40) cc_final: 0.5730 (tp40) REVERT: W 477 GLU cc_start: 0.7548 (mp0) cc_final: 0.7294 (mp0) REVERT: W 507 GLU cc_start: 0.6956 (tt0) cc_final: 0.6239 (tt0) REVERT: W 527 HIS cc_start: 0.7678 (m-70) cc_final: 0.7006 (m170) REVERT: W 542 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8087 (tp) REVERT: W 568 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: W 570 MET cc_start: 0.7465 (tpp) cc_final: 0.7090 (mpp) REVERT: W 589 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.6151 (tt) REVERT: W 599 ASP cc_start: 0.7800 (m-30) cc_final: 0.7276 (m-30) REVERT: W 614 ASP cc_start: 0.7977 (t0) cc_final: 0.7726 (t0) REVERT: W 629 THR cc_start: 0.8226 (t) cc_final: 0.7957 (m) REVERT: W 652 GLU cc_start: 0.7215 (pt0) cc_final: 0.6968 (pt0) REVERT: W 724 GLN cc_start: 0.7225 (tp40) cc_final: 0.6984 (tp40) REVERT: W 754 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7617 (mm-30) REVERT: W 761 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: W 766 LYS cc_start: 0.6365 (pttt) cc_final: 0.5964 (ptpp) REVERT: W 920 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6640 (pm20) REVERT: W 924 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7628 (mt-10) REVERT: W 1069 MET cc_start: 0.6904 (mmm) cc_final: 0.6664 (mmm) outliers start: 29 outliers final: 18 residues processed: 206 average time/residue: 0.1585 time to fit residues: 45.5761 Evaluate side-chains 216 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 82 LEU 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 F residue 92 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 114 VAL 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 542 LEU 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 702 VAL 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 1053 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 69 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 340 GLN ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 637 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.172737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130319 restraints weight = 27593.574| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.68 r_work: 0.3444 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19485 Z= 0.146 Angle : 0.627 9.425 27619 Z= 0.357 Chirality : 0.044 0.260 3067 Planarity : 0.004 0.050 2430 Dihedral : 29.054 178.252 5062 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.11 % Allowed : 16.77 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1462 helix: 1.49 (0.18), residues: 831 sheet: -0.36 (0.76), residues: 57 loop : -1.03 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 697 TYR 0.028 0.001 TYR W 374 PHE 0.012 0.001 PHE W 977 TRP 0.023 0.001 TRP W 491 HIS 0.006 0.001 HIS W 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (19485) covalent geometry : angle 0.62700 / 0.36 (27619) hydrogen bonds : bond 0.04429 / 2.92 ( 902) hydrogen bonds : angle 3.57761 / 2.57 ( 2362) ********************** 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 225 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.499 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 115 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7938 (mtmm) REVERT: C 29 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6905 (ttp-170) REVERT: D 56 MET cc_start: 0.7928 (mmm) cc_final: 0.7542 (mmm) REVERT: E 77 ASP cc_start: 0.8266 (t0) cc_final: 0.7952 (t0) REVERT: E 90 MET cc_start: 0.7195 (tpp) cc_final: 0.6872 (mpp) REVERT: F 84 MET cc_start: 0.7293 (mmm) cc_final: 0.6972 (mmm) REVERT: G 62 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7322 (tt) REVERT: G 73 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8008 (t0) REVERT: W 275 GLU cc_start: 0.6249 (tp30) cc_final: 0.5695 (tp30) REVERT: W 276 ARG cc_start: 0.6336 (ttt180) cc_final: 0.5444 (ttt90) REVERT: W 278 MET cc_start: 0.4484 (mmm) cc_final: 0.3990 (mmm) REVERT: W 312 GLU cc_start: 0.6450 (mp0) cc_final: 0.6212 (mp0) REVERT: W 320 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6577 (mt) REVERT: W 323 LYS cc_start: 0.7456 (tttt) cc_final: 0.6497 (ptmt) REVERT: W 386 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8305 (mtmt) REVERT: W 412 LYS cc_start: 0.6173 (tttm) cc_final: 0.5819 (ttpt) REVERT: W 432 LYS cc_start: 0.7589 (tptt) cc_final: 0.6759 (ttpt) REVERT: W 434 GLN cc_start: 0.6012 (tp40) cc_final: 0.5194 (tp40) REVERT: W 438 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6386 (m-30) REVERT: W 477 GLU cc_start: 0.7543 (mp0) cc_final: 0.7182 (mp0) REVERT: W 507 GLU cc_start: 0.6936 (tt0) cc_final: 0.6215 (tt0) REVERT: W 513 THR cc_start: 0.7116 (p) cc_final: 0.6714 (t) REVERT: W 527 HIS cc_start: 0.7618 (m-70) cc_final: 0.6957 (m170) REVERT: W 556 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7544 (mmm) REVERT: W 568 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: W 570 MET cc_start: 0.7352 (tpp) cc_final: 0.6959 (mpp) REVERT: W 599 ASP cc_start: 0.7739 (m-30) cc_final: 0.7153 (m-30) REVERT: W 614 ASP cc_start: 0.7974 (t0) cc_final: 0.7693 (t0) REVERT: W 629 THR cc_start: 0.8158 (t) cc_final: 0.7892 (m) REVERT: W 721 LEU cc_start: 0.8226 (mt) cc_final: 0.8022 (tp) REVERT: W 724 GLN cc_start: 0.7242 (tp40) cc_final: 0.7009 (tp40) REVERT: W 761 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6049 (t-90) REVERT: W 766 LYS cc_start: 0.6345 (pttt) cc_final: 0.5967 (ptpp) REVERT: W 964 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: W 1060 ARG cc_start: 0.7365 (tpp-160) cc_final: 0.6426 (tpp-160) REVERT: W 1069 MET cc_start: 0.6796 (mmm) cc_final: 0.6506 (mmm) outliers start: 27 outliers final: 15 residues processed: 213 average time/residue: 0.1744 time to fit residues: 52.2263 Evaluate side-chains 218 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain W residue 438 ASP 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 589 LEU Chi-restraints excluded: chain W residue 631 ILE Chi-restraints excluded: chain W residue 695 LEU Chi-restraints excluded: chain W residue 702 VAL Chi-restraints excluded: chain W residue 761 HIS Chi-restraints excluded: chain W residue 914 THR Chi-restraints excluded: chain W residue 964 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 92 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 4 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** W 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 GLN ** W 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 647 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.172969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130349 restraints weight = 27673.246| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.69 r_work: 0.3451 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19485 Z= 0.145 Angle : 0.619 10.824 27619 Z= 0.353 Chirality : 0.043 0.263 3067 Planarity : 0.004 0.049 2430 Dihedral : 28.982 178.931 5062 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 16.54 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1462 helix: 1.61 (0.18), residues: 829 sheet: -0.39 (0.76), residues: 57 loop : -0.97 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 697 TYR 0.035 0.001 TYR W 374 PHE 0.011 0.001 PHE W 748 TRP 0.023 0.001 TRP W 491 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (19485) covalent geometry : angle 0.61942 / 0.35 (27619) hydrogen bonds : bond 0.04343 / 2.88 ( 902) hydrogen bonds : angle 3.57350 / 2.56 ( 2362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4743.56 seconds wall clock time: 81 minutes 31.17 seconds (4891.17 seconds total)