Starting phenix.real_space_refine on Mon Jul 6 00:39:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqv_23489/07_2026/7lqv_23489.cif" } resolution = 3.25 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= -0.001 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 19854 2.51 5 N 5185 2.21 5 O 6091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.04s 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: 31274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8535 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 55, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8681 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 55, 'TRANS': 1056} Chain breaks: 3 Chain: "C" Number of atoms: 8500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8500 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 55, 'TRANS': 1031} Chain breaks: 4 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "W" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "X" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 775 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "Y" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Z" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 784 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.10, per 1000 atoms: 0.23 Number of scatterers: 31274 At special positions: 0 Unit cell: (198.904, 186.208, 203.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6091 8.00 N 5185 7.00 C 19854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 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 Links applied NAG-ASN " NAG A1306 " - " ASN A 603 " " NAG A1309 " - " ASN A 709 " " NAG B1303 " - " ASN B 331 " " NAG B1306 " - " ASN B 657 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 65 sheets defined 20.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.855A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 625 removed outlier: 3.681A pdb=" N HIS A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.602A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.769A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.786A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.254A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.577A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.174A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.666A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.839A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.637A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 3.823A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 631 through 636' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.850A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.519A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.764A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.506A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 855' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.891A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.386A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.615A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.283A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.641A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.031A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.980A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.614A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.934A pdb=" N VAL C 635 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.781A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.978A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 856 removed outlier: 3.712A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 856' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.859A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.318A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.524A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.401A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.964A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.774A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 4.037A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 100B through 100F removed outlier: 3.515A pdb=" N TYR H 100F" --> pdb=" O GLU H 100C" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.753A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 100B through 100F Processing helix chain 'X' and resid 79 through 83 removed outlier: 3.751A pdb=" N GLU X 83 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100B through 100F Processing helix chain 'Z' and resid 79 through 83 removed outlier: 3.607A pdb=" N GLU Z 83 " --> pdb=" O ALA Z 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.549A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.631A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.148A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.147A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 224 through 229 removed outlier: 5.446A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.548A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.615A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.553A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.791A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.328A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.562A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.629A pdb=" N HIS B 69 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.945A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.997A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.408A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.508A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 374 through 379 removed outlier: 4.543A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.531A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.331A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.528A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.410A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.646A pdb=" N HIS C 69 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 78 " --> pdb=" O HIS C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.214A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.794A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 225 through 229 removed outlier: 5.384A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.653A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 653 through 655 removed outlier: 5.953A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.297A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.853A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.717A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS H 22 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.643A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER H 112 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AF8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.914A pdb=" N ALA L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 97 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.626A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 5 through 6 removed outlier: 3.975A pdb=" N VAL W 20 " --> pdb=" O MET W 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET W 80 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA W 78 " --> pdb=" O CYS W 22 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP W 72 " --> pdb=" O THR W 77 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 10 through 13 removed outlier: 6.604A pdb=" N GLU W 10 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER W 112 " --> pdb=" O GLU W 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS W 12 " --> pdb=" O SER W 112 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR W 90 " --> pdb=" O THR W 107 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE W 34 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG W 50 " --> pdb=" O ILE W 34 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP W 36 " --> pdb=" O MET W 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET W 48 " --> pdb=" O TRP W 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 9 through 12 Processing sheet with id=AG4, first strand: chain 'X' and resid 9 through 12 removed outlier: 3.994A pdb=" N ALA X 90 " --> pdb=" O VAL X 97 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL X 97 " --> pdb=" O ALA X 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 19 through 24 removed outlier: 3.543A pdb=" N ALA X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 5 through 6 removed outlier: 3.851A pdb=" N VAL Y 20 " --> pdb=" O MET Y 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET Y 80 " --> pdb=" O VAL Y 20 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA Y 78 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP Y 72 " --> pdb=" O THR Y 77 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE Y 34 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG Y 50 " --> pdb=" O ILE Y 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TRP Y 36 " --> pdb=" O MET Y 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.615A pdb=" N GLU Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER Y 112 " --> pdb=" O GLU Y 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS Y 12 " --> pdb=" O SER Y 112 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Y 90 " --> pdb=" O THR Y 107 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL Y 102 " --> pdb=" O SER Y 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 9 through 13 Processing sheet with id=AH1, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.026A pdb=" N ALA Z 90 " --> pdb=" O VAL Z 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL Z 97 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 19 through 24 removed outlier: 3.578A pdb=" N ALA Z 19 " --> pdb=" O ILE Z 75 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.77 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7222 1.33 - 1.45: 7464 1.45 - 1.58: 17108 1.58 - 1.70: 1 1.70 - 1.83: 186 Bond restraints: 31981 Sorted by residual: bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.52e-02 4.33e+03 1.84e+01 bond pdb=" CB ASN A1134 " pdb=" CG ASN A1134 " ideal model delta sigma weight residual 1.516 1.582 -0.066 2.50e-02 1.60e+03 6.90e+00 bond pdb=" N ASP A 53 " pdb=" CA ASP A 53 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.16e-02 7.43e+03 5.70e+00 bond pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N LYS A 814 " pdb=" CA LYS A 814 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.12e-02 7.97e+03 5.33e+00 ... (remaining 31976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 42144 1.33 - 2.65: 1047 2.65 - 3.98: 259 3.98 - 5.31: 71 5.31 - 6.63: 11 Bond angle restraints: 43532 Sorted by residual: angle pdb=" CA ARG A 815 " pdb=" C ARG A 815 " pdb=" O ARG A 815 " ideal model delta sigma weight residual 121.88 116.39 5.49 1.13e+00 7.83e-01 2.36e+01 angle pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 121.19 116.49 4.70 1.10e+00 8.26e-01 1.83e+01 angle pdb=" N ALA A 522 " pdb=" CA ALA A 522 " pdb=" C ALA A 522 " ideal model delta sigma weight residual 107.73 113.94 -6.21 1.61e+00 3.86e-01 1.49e+01 angle pdb=" CA ASP A 53 " pdb=" C ASP A 53 " pdb=" O ASP A 53 " ideal model delta sigma weight residual 121.38 117.51 3.87 1.06e+00 8.90e-01 1.34e+01 angle pdb=" C THR A 51 " pdb=" CA THR A 51 " pdb=" CB THR A 51 " ideal model delta sigma weight residual 110.62 105.31 5.31 1.51e+00 4.39e-01 1.24e+01 ... (remaining 43527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17114 17.96 - 35.93: 1375 35.93 - 53.89: 251 53.89 - 71.85: 48 71.85 - 89.81: 32 Dihedral angle restraints: 18820 sinusoidal: 7272 harmonic: 11548 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -167.85 81.85 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 26.68 66.32 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 18817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3782 0.040 - 0.080: 729 0.080 - 0.120: 414 0.120 - 0.160: 60 0.160 - 0.200: 8 Chirality restraints: 4993 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU A 821 " pdb=" N LEU A 821 " pdb=" C LEU A 821 " pdb=" CB LEU A 821 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 4990 not shown) Planarity restraints: 5594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A1106 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" CD GLN A1106 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN A1106 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN A1106 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C1089 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO C1090 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C1090 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C1090 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 54 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C LEU A 54 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 54 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 55 " -0.011 2.00e-02 2.50e+03 ... (remaining 5591 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 363 2.60 - 3.17: 27614 3.17 - 3.75: 45904 3.75 - 4.32: 64638 4.32 - 4.90: 107725 Nonbonded interactions: 246244 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" O ALA A 522 " model vdw 2.020 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.040 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.067 3.040 nonbonded pdb=" OG SER B 816 " pdb=" OE1 GLU B 819 " model vdw 2.089 3.040 nonbonded pdb=" OE2 GLU C 654 " pdb=" OG SER C 691 " model vdw 2.098 3.040 ... (remaining 246239 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 14 through 827 or resid 853 through 1308)) selection = (chain 'B' and (resid 14 through 827 or resid 853 through 1308)) selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'L' and (resid 2 through 49 or resid 51 through 106A)) selection = chain 'X' selection = (chain 'Z' and (resid 2 through 49 or resid 51 through 106A)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.960 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 : 0.003 0.066 32034 Z= 0.151 Angle : 0.568 14.226 43642 Z= 0.299 Chirality : 0.043 0.200 4993 Planarity : 0.003 0.049 5590 Dihedral : 13.533 89.814 11265 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.41 (0.14), residues: 3938 helix: 1.82 (0.22), residues: 607 sheet: 0.08 (0.18), residues: 809 loop : -0.96 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.025 0.001 TYR C 508 PHE 0.015 0.001 PHE C 759 TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (31981) covalent geometry : angle 0.55645 / 0.30 (43532) SS BOND : bond 0.00317 / 0.22 ( 49) SS BOND : angle 1.05311 / 0.76 ( 98) hydrogen bonds : bond 0.25207 / 17.09 ( 1025) hydrogen bonds : angle 9.32726 / 6.45 ( 2817) link_NAG-ASN : bond 0.00990 / 0.50 ( 4) link_NAG-ASN : angle 6.40361 / 3.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ASN cc_start: 0.7560 (m-40) cc_final: 0.7339 (m-40) REVERT: C 1002 GLN cc_start: 0.8673 (tt0) cc_final: 0.8219 (tp-100) REVERT: W 100 TYR cc_start: 0.5571 (m-80) cc_final: 0.5237 (m-80) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.1709 time to fit residues: 55.1191 Evaluate side-chains 133 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 814 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 901 GLN A1134 ASN B 764 ASN B 804 GLN B1134 ASN C 935 GLN H 1 GLN H 39 GLN L 38 GLN L 50 GLN W 39 GLN Y 39 GLN Z 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.154529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099882 restraints weight = 83800.423| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.65 r_work: 0.3328 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32034 Z= 0.147 Angle : 0.596 9.068 43642 Z= 0.312 Chirality : 0.045 0.297 4993 Planarity : 0.004 0.048 5590 Dihedral : 4.138 54.933 4274 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.38 % Allowed : 5.38 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.44 (0.13), residues: 3938 helix: 1.68 (0.21), residues: 630 sheet: 0.14 (0.18), residues: 813 loop : -1.00 (0.13), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.021 0.001 TYR C1067 PHE 0.027 0.001 PHE A 168 TRP 0.016 0.001 TRP A 886 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (31981) covalent geometry : angle 0.58896 / 0.31 (43532) SS BOND : bond 0.00853 / 0.79 ( 49) SS BOND : angle 1.46148 / 1.12 ( 98) hydrogen bonds : bond 0.04841 / 3.29 ( 1025) hydrogen bonds : angle 6.77020 / 4.69 ( 2817) link_NAG-ASN : bond 0.00924 / 0.48 ( 4) link_NAG-ASN : angle 4.00551 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8774 (m-30) cc_final: 0.8556 (p0) REVERT: A 200 TYR cc_start: 0.7518 (m-10) cc_final: 0.7004 (m-80) REVERT: A 904 TYR cc_start: 0.7812 (t80) cc_final: 0.7526 (t80) REVERT: B 64 TRP cc_start: 0.8803 (t60) cc_final: 0.8558 (t60) REVERT: C 394 ASN cc_start: 0.8137 (m-40) cc_final: 0.7811 (t0) REVERT: C 697 MET cc_start: 0.8427 (ptp) cc_final: 0.8216 (ptm) REVERT: C 1002 GLN cc_start: 0.8960 (tt0) cc_final: 0.8388 (tp-100) REVERT: W 100 ILE cc_start: 0.5329 (mm) cc_final: 0.4657 (tt) REVERT: W 100 TYR cc_start: 0.5506 (m-80) cc_final: 0.4638 (m-80) outliers start: 13 outliers final: 5 residues processed: 171 average time/residue: 0.1554 time to fit residues: 46.2427 Evaluate side-chains 134 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain Z residue 50 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 146 optimal weight: 8.9990 chunk 339 optimal weight: 40.0000 chunk 333 optimal weight: 0.9990 chunk 104 optimal weight: 0.0770 chunk 77 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 394 ASN A 853 GLN B 955 ASN C 935 GLN L 38 GLN X 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.148508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.092625 restraints weight = 81825.835| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.85 r_work: 0.3296 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32034 Z= 0.133 Angle : 0.548 9.500 43642 Z= 0.286 Chirality : 0.044 0.301 4993 Planarity : 0.004 0.049 5590 Dihedral : 4.006 34.047 4270 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 0.73 % Allowed : 7.59 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.47 (0.13), residues: 3938 helix: 1.63 (0.21), residues: 635 sheet: 0.19 (0.18), residues: 809 loop : -1.04 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.023 0.001 TYR B 28 PHE 0.022 0.001 PHE B 192 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (31981) covalent geometry : angle 0.54015 / 0.28 (43532) SS BOND : bond 0.00337 / 0.24 ( 49) SS BOND : angle 1.62168 / 1.33 ( 98) hydrogen bonds : bond 0.04085 / 2.77 ( 1025) hydrogen bonds : angle 6.20749 / 4.31 ( 2817) link_NAG-ASN : bond 0.00820 / 0.43 ( 4) link_NAG-ASN : angle 3.50552 / 2.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7695 (m-10) cc_final: 0.7385 (m-80) REVERT: A 780 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 904 TYR cc_start: 0.7930 (t80) cc_final: 0.7604 (t80) REVERT: C 104 TRP cc_start: 0.7245 (m-90) cc_final: 0.6786 (m-90) REVERT: C 394 ASN cc_start: 0.7995 (m-40) cc_final: 0.7678 (t0) REVERT: C 780 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 1002 GLN cc_start: 0.9040 (tt0) cc_final: 0.8370 (tp-100) REVERT: H 48 MET cc_start: -0.1377 (tmm) cc_final: -0.1813 (ptm) REVERT: W 100 ILE cc_start: 0.5691 (mm) cc_final: 0.4965 (tt) REVERT: W 100 TYR cc_start: 0.5409 (m-80) cc_final: 0.4610 (m-10) REVERT: Z 24 SER cc_start: 0.6059 (p) cc_final: 0.5795 (t) outliers start: 25 outliers final: 11 residues processed: 182 average time/residue: 0.1579 time to fit residues: 50.0069 Evaluate side-chains 149 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain Z residue 50 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 189 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 370 optimal weight: 20.0000 chunk 200 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 331 optimal weight: 50.0000 chunk 281 optimal weight: 0.0470 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 762 GLN B 935 GLN B 955 ASN Z 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.145285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.088308 restraints weight = 82563.631| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 4.12 r_work: 0.3274 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 32034 Z= 0.154 Angle : 0.553 9.363 43642 Z= 0.286 Chirality : 0.044 0.303 4993 Planarity : 0.004 0.051 5590 Dihedral : 4.066 32.049 4270 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 0.99 % Allowed : 9.33 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.03 % 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: -0.50 (0.13), residues: 3938 helix: 1.58 (0.21), residues: 645 sheet: 0.04 (0.18), residues: 811 loop : -1.02 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.032 0.001 TYR Y 79 PHE 0.018 0.001 PHE A 823 TRP 0.017 0.001 TRP B 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (31981) covalent geometry : angle 0.54621 / 0.28 (43532) SS BOND : bond 0.00355 / 0.24 ( 49) SS BOND : angle 1.48786 / 1.14 ( 98) hydrogen bonds : bond 0.03734 / 2.55 ( 1025) hydrogen bonds : angle 5.90896 / 4.10 ( 2817) link_NAG-ASN : bond 0.00763 / 0.40 ( 4) link_NAG-ASN : angle 3.17401 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8863 (m-80) cc_final: 0.8564 (m-80) REVERT: A 88 ASP cc_start: 0.8809 (m-30) cc_final: 0.8565 (p0) REVERT: A 200 TYR cc_start: 0.7810 (m-10) cc_final: 0.7445 (m-10) REVERT: C 104 TRP cc_start: 0.7337 (m-90) cc_final: 0.7099 (m-90) REVERT: C 394 ASN cc_start: 0.7990 (m-40) cc_final: 0.7647 (t0) REVERT: C 780 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 1002 GLN cc_start: 0.9010 (tt0) cc_final: 0.8408 (tp-100) REVERT: W 100 ILE cc_start: 0.5370 (mm) cc_final: 0.4857 (tt) REVERT: W 100 TYR cc_start: 0.5414 (m-80) cc_final: 0.4515 (m-10) REVERT: Z 24 SER cc_start: 0.6145 (p) cc_final: 0.5833 (t) outliers start: 34 outliers final: 21 residues processed: 180 average time/residue: 0.1595 time to fit residues: 50.3075 Evaluate side-chains 149 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 223 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 373 optimal weight: 0.0060 chunk 187 optimal weight: 0.7980 chunk 270 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 349 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 955 ASN C 519 HIS Z 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.146226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.089131 restraints weight = 83652.350| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.23 r_work: 0.3309 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 32034 Z= 0.108 Angle : 0.526 9.479 43642 Z= 0.272 Chirality : 0.043 0.301 4993 Planarity : 0.004 0.053 5590 Dihedral : 3.965 33.596 4270 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 1.22 % Allowed : 10.26 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.47 (0.13), residues: 3938 helix: 1.56 (0.21), residues: 653 sheet: 0.03 (0.17), residues: 853 loop : -1.00 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.026 0.001 TYR A 904 PHE 0.018 0.001 PHE A 168 TRP 0.041 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (31981) covalent geometry : angle 0.52054 / 0.27 (43532) SS BOND : bond 0.00310 / 0.19 ( 49) SS BOND : angle 1.35129 / 0.96 ( 98) hydrogen bonds : bond 0.03478 / 2.36 ( 1025) hydrogen bonds : angle 5.71028 / 3.95 ( 2817) link_NAG-ASN : bond 0.00756 / 0.39 ( 4) link_NAG-ASN : angle 2.98084 / 1.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8834 (m-80) cc_final: 0.8478 (m-80) REVERT: A 88 ASP cc_start: 0.8811 (m-30) cc_final: 0.8589 (p0) REVERT: A 177 MET cc_start: 0.7217 (ppp) cc_final: 0.6991 (ppp) REVERT: A 200 TYR cc_start: 0.7785 (m-10) cc_final: 0.7400 (m-10) REVERT: A 904 TYR cc_start: 0.7763 (t80) cc_final: 0.7431 (t80) REVERT: B 314 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8541 (tm-30) REVERT: B 425 LEU cc_start: 0.0225 (OUTLIER) cc_final: -0.0456 (mt) REVERT: C 392 PHE cc_start: 0.7874 (m-80) cc_final: 0.7560 (m-10) REVERT: C 394 ASN cc_start: 0.7940 (m-40) cc_final: 0.7596 (t0) REVERT: C 1002 GLN cc_start: 0.9011 (tt0) cc_final: 0.8412 (tp-100) REVERT: W 100 ILE cc_start: 0.5385 (mm) cc_final: 0.4865 (tt) REVERT: W 100 TYR cc_start: 0.5448 (m-80) cc_final: 0.4526 (m-10) REVERT: Y 80 MET cc_start: -0.1060 (mmt) cc_final: -0.1313 (mmm) outliers start: 42 outliers final: 18 residues processed: 181 average time/residue: 0.1620 time to fit residues: 51.1349 Evaluate side-chains 153 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 156 optimal weight: 20.0000 chunk 362 optimal weight: 0.4980 chunk 168 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 340 optimal weight: 0.0050 chunk 63 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN B 955 ASN C 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.147776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.094978 restraints weight = 82065.472| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.51 r_work: 0.3319 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32034 Z= 0.102 Angle : 0.520 10.620 43642 Z= 0.268 Chirality : 0.043 0.304 4993 Planarity : 0.004 0.052 5590 Dihedral : 3.902 32.968 4270 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.61 % Favored : 94.34 % Rotamer: Outliers : 1.13 % Allowed : 11.45 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.40 (0.13), residues: 3938 helix: 1.70 (0.21), residues: 647 sheet: 0.08 (0.17), residues: 852 loop : -0.97 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 646 TYR 0.021 0.001 TYR C 28 PHE 0.018 0.001 PHE A 65 TRP 0.029 0.001 TRP A 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (31981) covalent geometry : angle 0.51545 / 0.27 (43532) SS BOND : bond 0.00278 / 0.17 ( 49) SS BOND : angle 1.21601 / 0.87 ( 98) hydrogen bonds : bond 0.03331 / 2.25 ( 1025) hydrogen bonds : angle 5.51235 / 3.81 ( 2817) link_NAG-ASN : bond 0.00748 / 0.39 ( 4) link_NAG-ASN : angle 2.88895 / 1.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7790 (m-10) cc_final: 0.7434 (m-10) REVERT: A 904 TYR cc_start: 0.7898 (t80) cc_final: 0.7550 (t80) REVERT: B 314 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 425 LEU cc_start: 0.0143 (OUTLIER) cc_final: -0.0517 (mt) REVERT: C 157 PHE cc_start: 0.7702 (m-10) cc_final: 0.7378 (m-10) REVERT: C 392 PHE cc_start: 0.7838 (m-80) cc_final: 0.7458 (m-10) REVERT: C 394 ASN cc_start: 0.7926 (m-40) cc_final: 0.7562 (t0) REVERT: C 780 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: C 1002 GLN cc_start: 0.9016 (tt0) cc_final: 0.8384 (tp-100) REVERT: W 100 ILE cc_start: 0.5658 (mm) cc_final: 0.5006 (tt) REVERT: W 100 TYR cc_start: 0.5450 (m-80) cc_final: 0.4463 (m-10) outliers start: 39 outliers final: 21 residues processed: 175 average time/residue: 0.1527 time to fit residues: 46.3348 Evaluate side-chains 156 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 230 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 359 optimal weight: 40.0000 chunk 231 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A1036 GLN B 955 ASN B1058 HIS B1074 ASN C 218 GLN C 544 ASN C 606 ASN C1074 ASN W 32 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.147188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090199 restraints weight = 84508.706| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.87 r_work: 0.3205 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32034 Z= 0.169 Angle : 0.554 9.359 43642 Z= 0.285 Chirality : 0.044 0.308 4993 Planarity : 0.004 0.055 5590 Dihedral : 4.025 33.778 4270 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 1.31 % Allowed : 12.03 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.50 (0.13), residues: 3938 helix: 1.60 (0.21), residues: 642 sheet: 0.00 (0.18), residues: 805 loop : -1.01 (0.13), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1014 TYR 0.028 0.001 TYR Y 79 PHE 0.017 0.001 PHE C 133 TRP 0.025 0.001 TRP A 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (31981) covalent geometry : angle 0.54901 / 0.28 (43532) SS BOND : bond 0.00357 / 0.23 ( 49) SS BOND : angle 1.42655 / 1.07 ( 98) hydrogen bonds : bond 0.03564 / 2.44 ( 1025) hydrogen bonds : angle 5.54147 / 3.85 ( 2817) link_NAG-ASN : bond 0.00737 / 0.39 ( 4) link_NAG-ASN : angle 2.85071 / 1.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8896 (m-30) cc_final: 0.8481 (p0) REVERT: A 200 TYR cc_start: 0.7959 (m-10) cc_final: 0.7677 (m-10) REVERT: A 904 TYR cc_start: 0.8165 (t80) cc_final: 0.7670 (t80) REVERT: B 425 LEU cc_start: 0.0161 (OUTLIER) cc_final: -0.0493 (mt) REVERT: B 990 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8508 (mt-10) REVERT: C 780 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: C 990 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: C 1002 GLN cc_start: 0.9127 (tt0) cc_final: 0.8447 (tp-100) REVERT: C 1111 GLU cc_start: 0.8710 (pm20) cc_final: 0.8492 (pm20) REVERT: W 100 ILE cc_start: 0.5499 (mm) cc_final: 0.4836 (tt) REVERT: W 100 TYR cc_start: 0.5270 (m-80) cc_final: 0.4292 (m-10) REVERT: Y 80 MET cc_start: 0.0022 (mmm) cc_final: -0.0870 (ppp) outliers start: 45 outliers final: 33 residues processed: 171 average time/residue: 0.1597 time to fit residues: 47.8369 Evaluate side-chains 166 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 301 optimal weight: 0.9990 chunk 391 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 316 optimal weight: 0.6980 chunk 229 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 955 ASN W 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088973 restraints weight = 82688.123| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.03 r_work: 0.3262 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32034 Z= 0.115 Angle : 0.522 9.452 43642 Z= 0.269 Chirality : 0.043 0.302 4993 Planarity : 0.004 0.065 5590 Dihedral : 3.924 34.308 4270 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 1.25 % Allowed : 12.21 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.45 (0.13), residues: 3938 helix: 1.62 (0.21), residues: 648 sheet: 0.09 (0.18), residues: 789 loop : -0.99 (0.13), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 646 TYR 0.017 0.001 TYR C1067 PHE 0.024 0.001 PHE A 65 TRP 0.020 0.001 TRP A 886 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (31981) covalent geometry : angle 0.51788 / 0.27 (43532) SS BOND : bond 0.00278 / 0.18 ( 49) SS BOND : angle 1.11939 / 0.84 ( 98) hydrogen bonds : bond 0.03285 / 2.24 ( 1025) hydrogen bonds : angle 5.40437 / 3.75 ( 2817) link_NAG-ASN : bond 0.00719 / 0.38 ( 4) link_NAG-ASN : angle 2.80346 / 1.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8959 (m-30) cc_final: 0.8641 (p0) REVERT: A 200 TYR cc_start: 0.7907 (m-10) cc_final: 0.7683 (m-80) REVERT: A 904 TYR cc_start: 0.8007 (t80) cc_final: 0.7611 (t80) REVERT: B 425 LEU cc_start: 0.0111 (OUTLIER) cc_final: -0.0526 (mt) REVERT: C 780 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: C 990 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 1002 GLN cc_start: 0.9048 (tt0) cc_final: 0.8416 (tp-100) REVERT: C 1050 MET cc_start: 0.8768 (ppp) cc_final: 0.8470 (ptm) REVERT: W 100 ILE cc_start: 0.5558 (mm) cc_final: 0.4971 (tt) REVERT: W 100 TYR cc_start: 0.5372 (m-80) cc_final: 0.4354 (m-10) REVERT: Y 80 MET cc_start: -0.0115 (mmm) cc_final: -0.1219 (ppp) outliers start: 43 outliers final: 28 residues processed: 169 average time/residue: 0.1690 time to fit residues: 50.2431 Evaluate side-chains 160 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 81 optimal weight: 0.8980 chunk 300 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 366 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 289 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.087745 restraints weight = 82447.737| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.25 r_work: 0.3243 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32034 Z= 0.146 Angle : 0.537 10.042 43642 Z= 0.276 Chirality : 0.044 0.306 4993 Planarity : 0.004 0.055 5590 Dihedral : 3.944 34.406 4270 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 1.08 % Allowed : 12.53 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.48 (0.14), residues: 3938 helix: 1.58 (0.21), residues: 647 sheet: -0.01 (0.18), residues: 809 loop : -0.98 (0.13), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.022 0.001 TYR C 904 PHE 0.014 0.001 PHE C1121 TRP 0.019 0.001 TRP A 886 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (31981) covalent geometry : angle 0.53280 / 0.27 (43532) SS BOND : bond 0.00313 / 0.20 ( 49) SS BOND : angle 1.21035 / 0.92 ( 98) hydrogen bonds : bond 0.03384 / 2.30 ( 1025) hydrogen bonds : angle 5.38504 / 3.73 ( 2817) link_NAG-ASN : bond 0.00710 / 0.37 ( 4) link_NAG-ASN : angle 2.80624 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8981 (m-30) cc_final: 0.8482 (p0) REVERT: A 200 TYR cc_start: 0.7938 (m-10) cc_final: 0.7689 (m-10) REVERT: A 904 TYR cc_start: 0.8080 (t80) cc_final: 0.7659 (t80) REVERT: B 425 LEU cc_start: 0.0166 (OUTLIER) cc_final: -0.0482 (mt) REVERT: B 990 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 780 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: C 990 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: C 1002 GLN cc_start: 0.9037 (tt0) cc_final: 0.8430 (tp-100) REVERT: W 100 ILE cc_start: 0.5701 (mm) cc_final: 0.5067 (tt) REVERT: W 100 TYR cc_start: 0.5411 (m-80) cc_final: 0.4346 (m-10) REVERT: Y 80 MET cc_start: 0.0696 (mmm) cc_final: -0.0295 (ppp) outliers start: 37 outliers final: 30 residues processed: 166 average time/residue: 0.1710 time to fit residues: 49.4029 Evaluate side-chains 157 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 240 optimal weight: 0.0010 chunk 324 optimal weight: 1.9990 chunk 169 optimal weight: 20.0000 chunk 278 optimal weight: 0.7980 chunk 319 optimal weight: 0.4980 chunk 245 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.146317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.092836 restraints weight = 83770.096| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.24 r_work: 0.3237 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32034 Z= 0.118 Angle : 0.530 11.251 43642 Z= 0.272 Chirality : 0.043 0.305 4993 Planarity : 0.004 0.058 5590 Dihedral : 3.908 34.980 4270 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 0.96 % Allowed : 12.59 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.43 (0.14), residues: 3938 helix: 1.67 (0.21), residues: 642 sheet: 0.06 (0.18), residues: 783 loop : -0.96 (0.13), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 646 TYR 0.026 0.001 TYR C 904 PHE 0.022 0.001 PHE A 65 TRP 0.018 0.001 TRP A 886 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (31981) covalent geometry : angle 0.52560 / 0.27 (43532) SS BOND : bond 0.00273 / 0.18 ( 49) SS BOND : angle 1.13464 / 0.87 ( 98) hydrogen bonds : bond 0.03267 / 2.22 ( 1025) hydrogen bonds : angle 5.32069 / 3.69 ( 2817) link_NAG-ASN : bond 0.00717 / 0.38 ( 4) link_NAG-ASN : angle 2.79429 / 1.83 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7876 Ramachandran restraints generated. 3938 Oldfield, 0 Emsley, 3938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8974 (m-30) cc_final: 0.8410 (p0) REVERT: A 200 TYR cc_start: 0.7999 (m-10) cc_final: 0.7725 (m-10) REVERT: A 904 TYR cc_start: 0.8188 (t80) cc_final: 0.7765 (t80) REVERT: B 425 LEU cc_start: 0.0247 (OUTLIER) cc_final: -0.0430 (mt) REVERT: C 780 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: C 990 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: C 1002 GLN cc_start: 0.9109 (tt0) cc_final: 0.8415 (tp-100) REVERT: W 100 ILE cc_start: 0.5675 (mm) cc_final: 0.5071 (tt) REVERT: W 100 TYR cc_start: 0.5470 (m-80) cc_final: 0.4399 (m-10) REVERT: Y 80 MET cc_start: 0.0727 (mmm) cc_final: -0.0281 (ppp) outliers start: 33 outliers final: 28 residues processed: 156 average time/residue: 0.1716 time to fit residues: 46.5156 Evaluate side-chains 155 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 130 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 355 optimal weight: 0.0270 chunk 148 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 322 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.144838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.090442 restraints weight = 83708.306| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.53 r_work: 0.3259 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32034 Z= 0.149 Angle : 0.541 10.708 43642 Z= 0.278 Chirality : 0.044 0.306 4993 Planarity : 0.004 0.054 5590 Dihedral : 3.939 35.293 4270 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.58 % Rotamer: Outliers : 1.05 % Allowed : 12.70 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -0.48 (0.13), residues: 3938 helix: 1.65 (0.21), residues: 641 sheet: -0.05 (0.18), residues: 782 loop : -0.97 (0.13), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.030 0.001 TYR C 904 PHE 0.017 0.001 PHE A 592 TRP 0.017 0.001 TRP A 886 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (31981) covalent geometry : angle 0.53613 / 0.28 (43532) SS BOND : bond 0.00311 / 0.19 ( 49) SS BOND : angle 1.31259 / 1.00 ( 98) hydrogen bonds : bond 0.03347 / 2.29 ( 1025) hydrogen bonds : angle 5.32767 / 3.70 ( 2817) link_NAG-ASN : bond 0.00701 / 0.37 ( 4) link_NAG-ASN : angle 2.80529 / 1.85 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10562.57 seconds wall clock time: 180 minutes 49.37 seconds (10849.37 seconds total)