Starting phenix.real_space_refine on Sat Feb 7 16:29:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.map" model { file = "/net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keo_37162/02_2026/8keo_37162.cif" } resolution = 2.78 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= 0.000 sd= 0.002 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 150 5.16 5 C 22119 2.51 5 N 5850 2.21 5 O 6669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34788 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8336 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 3 Chain: "A" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8336 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 3 Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "G" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "I" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "H" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8336 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 3 Time building chain proxies: 8.27, per 1000 atoms: 0.24 Number of scatterers: 34788 At special positions: 0 Unit cell: (154.7, 161.84, 270.13, 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 150 16.00 O 6669 8.00 N 5850 7.00 C 22119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 164 " 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 164 " 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=2.05 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=2.04 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 A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 106 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 106 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 85 sheets defined 16.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'B' and resid 258 through 262 removed outlier: 4.549A pdb=" N GLY B 261 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 262 " --> pdb=" O THR B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.591A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.265A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 754 removed outlier: 4.421A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.558A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.698A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.589A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.490A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.310A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 987 through 990 removed outlier: 3.687A pdb=" N GLU B 990 " --> pdb=" O PRO B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 990' Processing helix chain 'B' and resid 991 through 1033 removed outlier: 3.589A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.510A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.156A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.878A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.546A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 753 through 757 removed outlier: 3.625A pdb=" N TYR A 756 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 757' Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.607A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.653A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.610A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.486A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.262A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 990 removed outlier: 3.672A pdb=" N GLU A 990 " --> pdb=" O PRO A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 991 through 1033 removed outlier: 3.626A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'I' and resid 164 through 166 No H-bonds generated for 'chain 'I' and resid 164 through 166' Processing helix chain 'I' and resid 193 through 197 Processing helix chain 'H' and resid 122 through 129 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'C' and resid 258 through 262 removed outlier: 4.463A pdb=" N GLY C 261 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 262 " --> pdb=" O THR C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 258 through 262' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.517A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.022A pdb=" N ALA C 372 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.898A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 410' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.642A pdb=" N TYR C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.563A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.678A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.595A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.447A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.306A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.581A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.537A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.890A pdb=" N SER B 63 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 267 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR B 265 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 58 removed outlier: 3.922A pdb=" N ASP B 56 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 58 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.500A pdb=" N GLY B 108 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.630A pdb=" N LYS B 204 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 193 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 200 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.060A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 241 " --> pdb=" O GLY B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 130 removed outlier: 3.806A pdb=" N ILE B 129 " --> pdb=" O TYR B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.682A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AB1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.088A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.973A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.737A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.592A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.088A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.199A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.633A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.633A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.714A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.540A pdb=" N SER A 34 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 63 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 51 through 58 removed outlier: 3.983A pdb=" N ASP A 56 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 273 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 58 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 91 through 96 removed outlier: 3.650A pdb=" N LYS A 193 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 200 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 227 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 102 through 104 removed outlier: 3.518A pdb=" N GLY A 104 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AC7, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.850A pdb=" N ILE A 129 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.892A pdb=" N GLU A 133 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.645A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AD2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.906A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.851A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.732A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.630A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.865A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.620A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.620A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.661A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.543A pdb=" N CYS E 22 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.543A pdb=" N CYS E 22 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR E 80 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.747A pdb=" N THR E 120 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 92 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 97 " --> pdb=" O GLN E 35 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.747A pdb=" N THR E 120 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 92 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 112 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.773A pdb=" N LEU E 132 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY E 147 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 188 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL E 150 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 186 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER E 185 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA E 176 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER E 187 " --> pdb=" O PHE E 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 161 through 162 removed outlier: 3.630A pdb=" N SER E 161 " --> pdb=" O ASN E 205 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 4 through 5 removed outlier: 4.038A pdb=" N ARG D 24 " --> pdb=" O THR D 5 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 20 through 22 removed outlier: 3.997A pdb=" N ASP D 71 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.677A pdb=" N ASN D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 50 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN D 39 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.515A pdb=" N ASN D 138 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 179 " --> pdb=" O GLN D 161 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.091A pdb=" N LYS D 146 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 198 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 148 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 196 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 208 " --> pdb=" O CYS D 195 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 206 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.530A pdb=" N VAL G 5 " --> pdb=" O ARG G 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 22 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL G 18 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.530A pdb=" N VAL G 5 " --> pdb=" O ARG G 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS G 22 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 80 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.694A pdb=" N THR G 120 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 97 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.694A pdb=" N THR G 120 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE G 112 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.759A pdb=" N LEU G 132 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY G 147 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS G 148 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER G 188 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL G 150 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 186 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP G 152 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER G 185 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA G 176 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER G 187 " --> pdb=" O PHE G 174 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 161 through 162 removed outlier: 3.712A pdb=" N SER G 161 " --> pdb=" O ASN G 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN G 205 " --> pdb=" O SER G 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.058A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 20 through 22 removed outlier: 4.001A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.707A pdb=" N ASN F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR F 50 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU F 47 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLN F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F 39 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.607A pdb=" N VAL F 134 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR F 174 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F 179 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN F 161 " --> pdb=" O THR F 179 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.573A pdb=" N GLN F 156 " --> pdb=" O TRP F 149 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS F 146 " --> pdb=" O THR F 198 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR F 198 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 148 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU F 196 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS F 208 " --> pdb=" O CYS F 195 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL F 206 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.523A pdb=" N VAL I 5 " --> pdb=" O ARG I 23 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 18 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS I 22 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR I 80 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N THR I 120 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 92 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA I 97 " --> pdb=" O GLN I 35 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N THR I 120 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 92 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE I 112 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 128 through 132 removed outlier: 3.738A pdb=" N LEU I 132 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY I 147 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS I 148 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER I 188 " --> pdb=" O CYS I 148 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL I 150 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER I 185 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA I 176 " --> pdb=" O SER I 185 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER I 187 " --> pdb=" O PHE I 174 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 161 through 162 removed outlier: 3.749A pdb=" N SER I 161 " --> pdb=" O ASN I 205 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 4 through 5 removed outlier: 4.088A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 20 through 22 removed outlier: 3.991A pdb=" N ASP H 71 " --> pdb=" O SER H 68 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.725A pdb=" N ASN H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR H 50 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR H 88 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN H 39 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL H 86 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 115 through 119 removed outlier: 3.593A pdb=" N VAL H 134 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 179 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN H 161 " --> pdb=" O THR H 179 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 146 through 151 removed outlier: 4.156A pdb=" N LYS H 146 " --> pdb=" O THR H 198 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR H 198 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN H 148 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU H 196 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS H 208 " --> pdb=" O CYS H 195 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL H 206 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.650A pdb=" N SER C 34 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 63 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 267 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 51 through 58 removed outlier: 3.964A pdb=" N ASP C 56 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 58 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AH9, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.544A pdb=" N LYS C 204 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 193 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE C 199 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP C 228 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE C 201 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.896A pdb=" N GLY C 104 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.865A pdb=" N ILE C 129 " --> pdb=" O TYR C 168 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.555A pdb=" N ASN C 163 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.689A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.524A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 354 through 359 removed outlier: 3.860A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 354 through 359 removed outlier: 3.860A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.725A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.681A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.158A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.610A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 985 hydrogen bonds defined for protein. 2682 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: 9.31 Time building geometry restraints manager: 3.82 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: 9591 1.33 - 1.45: 6484 1.45 - 1.57: 19352 1.57 - 1.70: 0 1.70 - 1.82: 189 Bond restraints: 35616 Sorted by residual: bond pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 1.457 1.483 -0.027 6.40e-03 2.44e+04 1.73e+01 bond pdb=" N GLY B 526 " pdb=" CA GLY B 526 " ideal model delta sigma weight residual 1.434 1.483 -0.049 1.22e-02 6.72e+03 1.62e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.482 -0.027 7.00e-03 2.04e+04 1.45e+01 bond pdb=" N VAL B 510 " pdb=" CA VAL B 510 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.27e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.19e-02 7.06e+03 1.22e+01 ... (remaining 35611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 47524 2.04 - 4.08: 832 4.08 - 6.13: 86 6.13 - 8.17: 9 8.17 - 10.21: 2 Bond angle restraints: 48453 Sorted by residual: angle pdb=" N PRO C 337 " pdb=" CA PRO C 337 " pdb=" C PRO C 337 " ideal model delta sigma weight residual 112.48 102.84 9.64 1.35e+00 5.49e-01 5.10e+01 angle pdb=" N GLU C 340 " pdb=" CA GLU C 340 " pdb=" C GLU C 340 " ideal model delta sigma weight residual 110.10 99.89 10.21 1.49e+00 4.50e-01 4.70e+01 angle pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" O CYS A 525 " ideal model delta sigma weight residual 121.89 115.73 6.16 1.27e+00 6.20e-01 2.35e+01 angle pdb=" CA PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 117.59 122.33 -4.74 9.90e-01 1.02e+00 2.29e+01 angle pdb=" CA GLU C 340 " pdb=" C GLU C 340 " pdb=" O GLU C 340 " ideal model delta sigma weight residual 120.92 115.62 5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 48448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 20349 17.57 - 35.15: 674 35.15 - 52.72: 153 52.72 - 70.30: 64 70.30 - 87.87: 12 Dihedral angle restraints: 21252 sinusoidal: 8274 harmonic: 12978 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 177.27 -84.27 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.20 49.20 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA HIS C 144 " pdb=" C HIS C 144 " pdb=" N LYS C 145 " pdb=" CA LYS C 145 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 21249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4701 0.067 - 0.133: 656 0.133 - 0.200: 60 0.200 - 0.266: 21 0.266 - 0.333: 7 Chirality restraints: 5445 Sorted by residual: chirality pdb=" CA GLU C 340 " pdb=" N GLU C 340 " pdb=" C GLU C 340 " pdb=" CB GLU C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA LYS B 529 " pdb=" N LYS B 529 " pdb=" C LYS B 529 " pdb=" CB LYS B 529 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN A 536 " pdb=" N ASN A 536 " pdb=" C ASN A 536 " pdb=" CB ASN A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5442 not shown) Planarity restraints: 6273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 204 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C LYS B 204 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS B 204 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS B 205 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 504 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C GLY B 504 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY B 504 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS B 505 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLU C 340 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU C 340 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL C 341 " 0.012 2.00e-02 2.50e+03 ... (remaining 6270 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8729 2.80 - 3.32: 29731 3.32 - 3.85: 53580 3.85 - 4.37: 59738 4.37 - 4.90: 105112 Nonbonded interactions: 256890 Sorted by model distance: nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.289 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.291 3.040 ... (remaining 256885 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 35.140 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 0.049 35663 Z= 0.237 Angle : 0.571 10.210 48547 Z= 0.364 Chirality : 0.048 0.333 5445 Planarity : 0.003 0.046 6273 Dihedral : 9.593 87.874 12777 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.26 % Favored : 94.63 % Rotamer: Outliers : 4.93 % Allowed : 6.66 % Favored : 88.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.11), residues: 4431 helix: 0.28 (0.21), residues: 634 sheet: -1.68 (0.15), residues: 1076 loop : -3.53 (0.09), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.011 0.001 TYR C 508 PHE 0.016 0.001 PHE C 338 TRP 0.005 0.000 TRP I 47 HIS 0.004 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00334 (35616) covalent geometry : angle 0.56930 (48453) SS BOND : bond 0.00581 ( 47) SS BOND : angle 1.12339 ( 94) hydrogen bonds : bond 0.26706 ( 935) hydrogen bonds : angle 8.17310 ( 2682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 347 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8009 (p) REVERT: B 998 THR cc_start: 0.9031 (m) cc_final: 0.8810 (p) REVERT: B 1010 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8691 (mp10) REVERT: B 1034 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8795 (pp) REVERT: A 68 PHE cc_start: 0.7210 (m-80) cc_final: 0.6816 (m-10) REVERT: A 128 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7915 (m) REVERT: A 229 LEU cc_start: 0.9268 (mt) cc_final: 0.8932 (tt) REVERT: A 307 THR cc_start: 0.9404 (OUTLIER) cc_final: 0.9076 (p) REVERT: A 339 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8621 (p0) REVERT: A 501 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: A 532 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8775 (t0) REVERT: A 537 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8877 (tptm) REVERT: E 80 TYR cc_start: 0.9294 (m-80) cc_final: 0.8660 (m-10) REVERT: E 184 TYR cc_start: 0.8576 (m-80) cc_final: 0.8327 (m-10) REVERT: D 48 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6282 (pp) REVERT: D 62 ARG cc_start: 0.7522 (ptt-90) cc_final: 0.6573 (tmm-80) REVERT: G 2 MET cc_start: 0.3406 (ttt) cc_final: 0.3068 (ptm) REVERT: I 2 MET cc_start: 0.1272 (ttt) cc_final: 0.0028 (ttt) REVERT: I 63 LYS cc_start: 0.8016 (tttt) cc_final: 0.7609 (pmtt) REVERT: I 74 MET cc_start: 0.5179 (mtp) cc_final: 0.4806 (tpt) REVERT: I 87 ARG cc_start: 0.8361 (ptm-80) cc_final: 0.7939 (mmp80) REVERT: I 204 CYS cc_start: 0.6318 (p) cc_final: 0.5983 (t) REVERT: H 71 ASP cc_start: 0.6231 (t70) cc_final: 0.5600 (m-30) REVERT: C 128 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7819 (m) REVERT: C 206 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8643 (p) REVERT: C 229 LEU cc_start: 0.9072 (mt) cc_final: 0.8758 (tm) REVERT: C 265 TYR cc_start: 0.5577 (t80) cc_final: 0.5334 (t80) REVERT: C 338 PHE cc_start: 0.6941 (p90) cc_final: 0.6510 (p90) REVERT: C 532 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8904 (t0) outliers start: 192 outliers final: 26 residues processed: 514 average time/residue: 0.7216 time to fit residues: 441.8260 Evaluate side-chains 176 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 123 ASN B 126 ASN B 162 ASN B 183 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 280 ASN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 540 ASN B 563 GLN B 580 GLN B 613 GLN B 677 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 901 GLN B 913 GLN B 914 ASN B 949 GLN B 957 GLN B 965 GLN B1010 GLN B1011 GLN B1048 HIS B1125 ASN A 123 ASN A 162 ASN A 183 ASN A 205 HIS A 218 GLN A 280 ASN A 414 GLN A 422 ASN A 532 ASN A 563 GLN A 613 GLN A 784 GLN A 901 GLN A 913 GLN A 914 ASN A 949 GLN A 957 GLN A 965 GLN A1005 GLN A1011 GLN A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN A1125 ASN E 62 GLN E 200 GLN D 90 GLN D 91 GLN D 101 GLN G 62 GLN G 105 ASN G 115 GLN G 179 GLN G 200 GLN F 90 GLN F 91 GLN F 101 GLN F 125 GLN I 115 GLN I 179 GLN I 200 GLN H 27 GLN H 43 GLN H 90 GLN H 91 GLN H 101 GLN H 167 GLN C 88 ASN C 123 ASN C 126 ASN C 162 ASN C 183 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 245 HIS C 280 ASN C 414 GLN C 422 ASN C 532 ASN C 536 ASN C 540 ASN C 563 GLN C 580 GLN C 613 GLN C 690 GLN C 784 GLN C 901 GLN C 913 GLN C 914 ASN C 949 GLN C 957 GLN C 965 GLN C1011 GLN C1048 HIS C1088 HIS C1125 ASN Total number of N/Q/H flips: 99 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.112672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.074356 restraints weight = 170608.020| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 6.02 r_work: 0.2898 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35663 Z= 0.235 Angle : 0.664 8.928 48547 Z= 0.344 Chirality : 0.046 0.248 5445 Planarity : 0.005 0.052 6273 Dihedral : 5.282 58.569 4896 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 3.08 % Allowed : 11.87 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.12), residues: 4431 helix: 0.98 (0.21), residues: 656 sheet: -1.36 (0.14), residues: 1148 loop : -3.20 (0.10), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 67 TYR 0.033 0.002 TYR B 365 PHE 0.024 0.002 PHE B 802 TRP 0.025 0.001 TRP F 36 HIS 0.011 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00548 (35616) covalent geometry : angle 0.66340 (48453) SS BOND : bond 0.00289 ( 47) SS BOND : angle 0.91036 ( 94) hydrogen bonds : bond 0.05799 ( 935) hydrogen bonds : angle 5.52271 ( 2682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 133 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 678 THR cc_start: 0.7154 (OUTLIER) cc_final: 0.6826 (m) REVERT: B 1010 GLN cc_start: 0.9560 (OUTLIER) cc_final: 0.9356 (mp10) REVERT: A 36 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9445 (p) REVERT: A 80 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: A 229 LEU cc_start: 0.9391 (mt) cc_final: 0.8895 (tt) REVERT: A 265 TYR cc_start: 0.6578 (t80) cc_final: 0.6377 (t80) REVERT: A 307 THR cc_start: 0.9602 (OUTLIER) cc_final: 0.9365 (p) REVERT: A 339 ASP cc_start: 0.9491 (OUTLIER) cc_final: 0.9181 (p0) REVERT: A 537 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8554 (tptm) REVERT: A 740 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9024 (tpt) REVERT: A 1010 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9245 (mp10) REVERT: A 1031 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8830 (mm-30) REVERT: E 2 MET cc_start: 0.6717 (tmt) cc_final: 0.5819 (tmt) REVERT: E 74 MET cc_start: 0.8577 (mmm) cc_final: 0.8317 (mmp) REVERT: G 2 MET cc_start: 0.6500 (ttt) cc_final: 0.6138 (ptm) REVERT: G 11 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7213 (t) REVERT: G 82 GLU cc_start: 0.7765 (tt0) cc_final: 0.7256 (tp30) REVERT: G 103 ARG cc_start: 0.8378 (mpp-170) cc_final: 0.7838 (mmp80) REVERT: I 63 LYS cc_start: 0.8134 (tttt) cc_final: 0.7910 (pmtt) REVERT: I 74 MET cc_start: 0.6587 (mtp) cc_final: 0.5965 (tpt) REVERT: I 81 MET cc_start: -0.2617 (ttp) cc_final: -0.2935 (tmm) REVERT: H 80 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7137 (pt0) REVERT: C 175 MET cc_start: 0.7780 (tmm) cc_final: 0.7197 (ptm) REVERT: C 532 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.9007 (t0) outliers start: 120 outliers final: 41 residues processed: 244 average time/residue: 0.6674 time to fit residues: 198.0153 Evaluate side-chains 155 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 290 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 427 optimal weight: 4.9990 chunk 437 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 215 optimal weight: 40.0000 chunk 56 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 245 HIS B 703 ASN B 901 GLN A 205 HIS A 245 HIS A 540 ASN A 580 GLN A 703 ASN A 901 GLN ** E 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 331 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 804 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.104468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059530 restraints weight = 150433.656| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.69 r_work: 0.2889 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35663 Z= 0.208 Angle : 0.586 8.083 48547 Z= 0.306 Chirality : 0.044 0.218 5445 Planarity : 0.004 0.046 6273 Dihedral : 4.821 72.267 4862 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.79 % Favored : 93.18 % Rotamer: Outliers : 2.60 % Allowed : 12.90 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.12), residues: 4431 helix: 1.44 (0.22), residues: 656 sheet: -1.12 (0.14), residues: 1193 loop : -2.86 (0.11), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.027 0.001 TYR A 904 PHE 0.017 0.002 PHE B1052 TRP 0.013 0.001 TRP B 105 HIS 0.027 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00485 (35616) covalent geometry : angle 0.58624 (48453) SS BOND : bond 0.00196 ( 47) SS BOND : angle 0.67187 ( 94) hydrogen bonds : bond 0.05644 ( 935) hydrogen bonds : angle 5.13699 ( 2682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 105 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 THR cc_start: 0.5678 (OUTLIER) cc_final: 0.5432 (p) REVERT: B 1010 GLN cc_start: 0.9499 (OUTLIER) cc_final: 0.9186 (mp10) REVERT: A 36 THR cc_start: 0.9694 (OUTLIER) cc_final: 0.9471 (p) REVERT: A 44 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8640 (mtpp) REVERT: A 80 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: A 175 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7406 (ptm) REVERT: A 205 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8643 (t70) REVERT: A 307 THR cc_start: 0.9614 (OUTLIER) cc_final: 0.9368 (p) REVERT: A 339 ASP cc_start: 0.9545 (OUTLIER) cc_final: 0.9255 (p0) REVERT: A 1031 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8791 (mm-30) REVERT: E 67 ARG cc_start: 0.5343 (ppt90) cc_final: 0.4974 (ppt90) REVERT: G 2 MET cc_start: 0.5756 (ttt) cc_final: 0.5142 (ptm) REVERT: G 82 GLU cc_start: 0.7642 (tt0) cc_final: 0.7439 (tp30) REVERT: G 103 ARG cc_start: 0.8438 (mpp-170) cc_final: 0.8237 (mpp-170) REVERT: I 2 MET cc_start: 0.4711 (ttt) cc_final: 0.4497 (ttt) REVERT: I 74 MET cc_start: 0.5975 (mtp) cc_final: 0.5496 (tpt) REVERT: I 81 MET cc_start: -0.2208 (ttp) cc_final: -0.2569 (tmm) REVERT: C 175 MET cc_start: 0.7890 (tmm) cc_final: 0.7338 (ptt) REVERT: C 340 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: C 532 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.9073 (t0) REVERT: C 697 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8987 (ptm) REVERT: C 745 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8725 (p0) REVERT: C 759 PHE cc_start: 0.8803 (m-80) cc_final: 0.8501 (m-80) REVERT: C 811 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (ptpp) outliers start: 101 outliers final: 33 residues processed: 196 average time/residue: 0.5963 time to fit residues: 143.4287 Evaluate side-chains 141 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 93 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 434 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 441 optimal weight: 0.8980 chunk 249 optimal weight: 50.0000 chunk 286 optimal weight: 50.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 901 GLN A 205 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.111624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.071824 restraints weight = 169404.667| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 6.60 r_work: 0.2846 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35663 Z= 0.150 Angle : 0.538 7.767 48547 Z= 0.277 Chirality : 0.042 0.176 5445 Planarity : 0.004 0.046 6273 Dihedral : 4.567 59.672 4845 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 2.34 % Allowed : 13.42 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.12), residues: 4431 helix: 1.66 (0.22), residues: 661 sheet: -0.92 (0.14), residues: 1226 loop : -2.77 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.019 0.001 TYR C 904 PHE 0.016 0.001 PHE F 140 TRP 0.013 0.001 TRP F 36 HIS 0.011 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00354 (35616) covalent geometry : angle 0.53726 (48453) SS BOND : bond 0.00204 ( 47) SS BOND : angle 0.65814 ( 94) hydrogen bonds : bond 0.04834 ( 935) hydrogen bonds : angle 4.82092 ( 2682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 95 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1010 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.9209 (mp10) REVERT: A 36 THR cc_start: 0.9704 (OUTLIER) cc_final: 0.9488 (p) REVERT: A 44 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8647 (mtpp) REVERT: A 80 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: A 307 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9408 (p) REVERT: A 339 ASP cc_start: 0.9527 (OUTLIER) cc_final: 0.9271 (p0) REVERT: A 853 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6506 (pp30) REVERT: A 1031 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (mm-30) REVERT: E 2 MET cc_start: 0.6776 (tmt) cc_final: 0.6466 (tmm) REVERT: D 84 PHE cc_start: 0.1049 (OUTLIER) cc_final: 0.0730 (t80) REVERT: I 74 MET cc_start: 0.6554 (mtp) cc_final: 0.6047 (tpt) REVERT: I 81 MET cc_start: -0.2141 (ttp) cc_final: -0.2499 (tmm) REVERT: H 80 GLU cc_start: 0.7499 (tp30) cc_final: 0.6731 (pt0) REVERT: C 175 MET cc_start: 0.7972 (tmm) cc_final: 0.7286 (ptm) REVERT: C 242 LEU cc_start: 0.9008 (tp) cc_final: 0.8740 (mp) REVERT: C 340 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: C 532 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.9020 (t0) REVERT: C 745 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8599 (p0) REVERT: C 759 PHE cc_start: 0.8752 (m-80) cc_final: 0.8401 (m-80) REVERT: C 811 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8274 (ptpp) outliers start: 91 outliers final: 36 residues processed: 182 average time/residue: 0.5941 time to fit residues: 134.0944 Evaluate side-chains 141 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 430 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 282 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 267 optimal weight: 40.0000 chunk 196 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 403 optimal weight: 0.0170 chunk 358 optimal weight: 9.9990 chunk 438 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS A 186 ASN A 422 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.106598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063090 restraints weight = 151331.851| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 4.38 r_work: 0.2949 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35663 Z= 0.096 Angle : 0.498 7.053 48547 Z= 0.255 Chirality : 0.042 0.170 5445 Planarity : 0.003 0.044 6273 Dihedral : 4.373 58.973 4843 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 2.13 % Allowed : 13.60 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.12), residues: 4431 helix: 1.91 (0.22), residues: 660 sheet: -0.70 (0.15), residues: 1199 loop : -2.59 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 87 TYR 0.021 0.001 TYR A 904 PHE 0.025 0.001 PHE A 68 TRP 0.012 0.001 TRP F 36 HIS 0.011 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00222 (35616) covalent geometry : angle 0.49838 (48453) SS BOND : bond 0.00169 ( 47) SS BOND : angle 0.51251 ( 94) hydrogen bonds : bond 0.03842 ( 935) hydrogen bonds : angle 4.48077 ( 2682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 98 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (tm) REVERT: B 242 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 587 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8695 (pp) REVERT: B 1010 GLN cc_start: 0.9462 (OUTLIER) cc_final: 0.9173 (mp10) REVERT: A 36 THR cc_start: 0.9676 (OUTLIER) cc_final: 0.9461 (p) REVERT: A 44 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8562 (mtpp) REVERT: A 307 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9412 (p) REVERT: A 853 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6522 (pp30) REVERT: E 2 MET cc_start: 0.6156 (tmt) cc_final: 0.5752 (tmm) REVERT: E 67 ARG cc_start: 0.5608 (ppt90) cc_final: 0.5152 (ppt90) REVERT: D 84 PHE cc_start: 0.0606 (OUTLIER) cc_final: -0.0069 (t80) REVERT: G 11 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.7005 (t) REVERT: G 103 ARG cc_start: 0.8644 (mpp-170) cc_final: 0.7755 (mmm160) REVERT: F 11 LEU cc_start: 0.2155 (OUTLIER) cc_final: 0.1840 (mp) REVERT: I 74 MET cc_start: 0.6474 (mtp) cc_final: 0.5960 (tpt) REVERT: I 81 MET cc_start: -0.2112 (ttp) cc_final: -0.2515 (tmm) REVERT: I 87 ARG cc_start: 0.8730 (ptm-80) cc_final: 0.7991 (mmm160) REVERT: H 80 GLU cc_start: 0.7494 (tp30) cc_final: 0.6730 (pt0) REVERT: C 175 MET cc_start: 0.7985 (tmm) cc_final: 0.7536 (ptm) REVERT: C 242 LEU cc_start: 0.9033 (tp) cc_final: 0.8684 (mp) REVERT: C 532 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.9038 (t0) REVERT: C 745 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8648 (OUTLIER) REVERT: C 811 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8146 (ptpp) REVERT: C 1050 MET cc_start: 0.8517 (mtp) cc_final: 0.8275 (mtp) outliers start: 83 outliers final: 33 residues processed: 177 average time/residue: 0.5620 time to fit residues: 123.9489 Evaluate side-chains 137 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 338 optimal weight: 10.0000 chunk 399 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 417 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 389 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 965 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN C 147 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.062253 restraints weight = 141477.859| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 5.38 r_work: 0.2817 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 35663 Z= 0.259 Angle : 0.625 9.546 48547 Z= 0.325 Chirality : 0.044 0.196 5445 Planarity : 0.004 0.044 6273 Dihedral : 4.744 59.463 4841 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.72 % Rotamer: Outliers : 2.65 % Allowed : 13.80 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4431 helix: 1.40 (0.21), residues: 667 sheet: -0.69 (0.14), residues: 1250 loop : -2.56 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1107 TYR 0.021 0.001 TYR C 904 PHE 0.020 0.002 PHE A1042 TRP 0.014 0.001 TRP A 886 HIS 0.012 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00611 (35616) covalent geometry : angle 0.62450 (48453) SS BOND : bond 0.00236 ( 47) SS BOND : angle 0.73878 ( 94) hydrogen bonds : bond 0.06409 ( 935) hydrogen bonds : angle 4.97280 ( 2682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 92 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8130 (tm) REVERT: B 242 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8995 (tm) REVERT: B 587 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 1010 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.9221 (mp10) REVERT: A 68 PHE cc_start: 0.8822 (m-80) cc_final: 0.8599 (m-10) REVERT: A 205 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7955 (t-90) REVERT: A 853 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6406 (pp30) REVERT: E 2 MET cc_start: 0.6257 (tmt) cc_final: 0.5684 (tmm) REVERT: E 74 MET cc_start: 0.8371 (mmm) cc_final: 0.8068 (mmm) REVERT: G 2 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5047 (ppp) REVERT: F 11 LEU cc_start: 0.2409 (OUTLIER) cc_final: 0.2118 (mp) REVERT: I 74 MET cc_start: 0.6352 (mtp) cc_final: 0.6087 (tpp) REVERT: I 81 MET cc_start: -0.2082 (ttp) cc_final: -0.2446 (tmm) REVERT: H 17 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.4991 (pp20) REVERT: C 175 MET cc_start: 0.8008 (tmm) cc_final: 0.7663 (ptt) REVERT: C 697 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9073 (ptm) REVERT: C 745 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8525 (p0) REVERT: C 811 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8360 (ptpp) outliers start: 103 outliers final: 50 residues processed: 185 average time/residue: 0.5922 time to fit residues: 136.2550 Evaluate side-chains 147 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 85 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 151 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 294 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 chunk 392 optimal weight: 0.7980 chunk 280 optimal weight: 50.0000 chunk 59 optimal weight: 0.2980 chunk 287 optimal weight: 30.0000 chunk 362 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 416 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 965 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 205 HIS A 901 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.111486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.072047 restraints weight = 169169.252| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 6.31 r_work: 0.2863 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 35663 Z= 0.101 Angle : 0.518 9.920 48547 Z= 0.264 Chirality : 0.042 0.203 5445 Planarity : 0.003 0.043 6273 Dihedral : 4.288 57.216 4837 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 2.00 % Allowed : 14.52 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4431 helix: 1.94 (0.22), residues: 653 sheet: -0.45 (0.15), residues: 1229 loop : -2.42 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.015 0.001 TYR C 265 PHE 0.020 0.001 PHE F 140 TRP 0.010 0.001 TRP F 36 HIS 0.011 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00237 (35616) covalent geometry : angle 0.51796 (48453) SS BOND : bond 0.00179 ( 47) SS BOND : angle 0.51239 ( 94) hydrogen bonds : bond 0.04102 ( 935) hydrogen bonds : angle 4.44254 ( 2682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 97 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (tm) REVERT: B 242 LEU cc_start: 0.9236 (mp) cc_final: 0.8933 (tm) REVERT: B 587 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8553 (pp) REVERT: B 1010 GLN cc_start: 0.9458 (OUTLIER) cc_final: 0.9180 (mp10) REVERT: A 68 PHE cc_start: 0.8715 (m-80) cc_final: 0.8431 (m-10) REVERT: A 205 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8255 (t-90) REVERT: A 565 PHE cc_start: 0.8975 (m-10) cc_final: 0.8775 (m-10) REVERT: E 2 MET cc_start: 0.7382 (tmt) cc_final: 0.6951 (tmm) REVERT: E 67 ARG cc_start: 0.5234 (ppt90) cc_final: 0.4912 (ppt90) REVERT: G 2 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5976 (ppp) REVERT: I 2 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6012 (ppp) REVERT: I 74 MET cc_start: 0.6785 (mtp) cc_final: 0.6356 (mmt) REVERT: I 81 MET cc_start: -0.2107 (ttp) cc_final: -0.2401 (tmm) REVERT: I 87 ARG cc_start: 0.8652 (ptm-80) cc_final: 0.7942 (mmm160) REVERT: H 80 GLU cc_start: 0.6962 (tp30) cc_final: 0.6454 (mt-10) REVERT: C 151 MET cc_start: 0.7683 (pmm) cc_final: 0.7206 (pmm) REVERT: C 175 MET cc_start: 0.8175 (tmm) cc_final: 0.7690 (ptt) REVERT: C 242 LEU cc_start: 0.8661 (tp) cc_final: 0.8061 (mp) REVERT: C 697 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9005 (ptm) REVERT: C 811 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8244 (ptpp) outliers start: 78 outliers final: 34 residues processed: 164 average time/residue: 0.6707 time to fit residues: 134.7715 Evaluate side-chains 136 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 328 optimal weight: 40.0000 chunk 421 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 395 optimal weight: 7.9990 chunk 274 optimal weight: 0.0770 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 441 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN B 965 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.110920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.071312 restraints weight = 169295.667| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 5.87 r_work: 0.2840 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35663 Z= 0.134 Angle : 0.532 11.585 48547 Z= 0.271 Chirality : 0.042 0.258 5445 Planarity : 0.003 0.052 6273 Dihedral : 4.169 57.199 4834 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.73 % Favored : 93.23 % Rotamer: Outliers : 1.82 % Allowed : 14.73 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 4431 helix: 1.90 (0.22), residues: 653 sheet: -0.29 (0.15), residues: 1203 loop : -2.36 (0.11), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.023 0.001 TYR G 80 PHE 0.019 0.001 PHE F 140 TRP 0.008 0.001 TRP F 36 HIS 0.012 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00320 (35616) covalent geometry : angle 0.53238 (48453) SS BOND : bond 0.00168 ( 47) SS BOND : angle 0.50964 ( 94) hydrogen bonds : bond 0.04441 ( 935) hydrogen bonds : angle 4.43849 ( 2682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 97 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8222 (tm) REVERT: B 242 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8948 (tm) REVERT: B 587 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8503 (pp) REVERT: B 1010 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.9193 (mp10) REVERT: A 68 PHE cc_start: 0.8778 (m-80) cc_final: 0.8465 (m-10) REVERT: A 449 TYR cc_start: 0.9189 (t80) cc_final: 0.8560 (m-80) REVERT: E 2 MET cc_start: 0.7355 (tmt) cc_final: 0.6853 (tmt) REVERT: E 67 ARG cc_start: 0.5327 (ppt90) cc_final: 0.4869 (ppt90) REVERT: G 2 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5823 (ppp) REVERT: G 103 ARG cc_start: 0.8410 (mmp-170) cc_final: 0.8139 (mmp80) REVERT: I 2 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.5737 (ppp) REVERT: I 74 MET cc_start: 0.6644 (mtp) cc_final: 0.6324 (mmt) REVERT: I 81 MET cc_start: -0.2071 (ttp) cc_final: -0.2429 (tmm) REVERT: C 136 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8446 (t80) REVERT: C 175 MET cc_start: 0.8063 (tmm) cc_final: 0.7780 (ptt) REVERT: C 242 LEU cc_start: 0.8708 (tp) cc_final: 0.8086 (mp) REVERT: C 697 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9013 (ptm) REVERT: C 811 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8348 (ptpp) outliers start: 71 outliers final: 40 residues processed: 162 average time/residue: 0.6499 time to fit residues: 128.8255 Evaluate side-chains 135 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 342 optimal weight: 20.0000 chunk 418 optimal weight: 3.9990 chunk 335 optimal weight: 40.0000 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 281 optimal weight: 50.0000 chunk 227 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 417 optimal weight: 0.9980 chunk 336 optimal weight: 40.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.103266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.059423 restraints weight = 152265.109| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.10 r_work: 0.2859 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35663 Z= 0.195 Angle : 0.585 13.769 48547 Z= 0.299 Chirality : 0.043 0.255 5445 Planarity : 0.004 0.047 6273 Dihedral : 4.254 56.881 4832 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 1.75 % Allowed : 14.83 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 4431 helix: 1.67 (0.22), residues: 662 sheet: -0.35 (0.15), residues: 1233 loop : -2.32 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 87 TYR 0.019 0.001 TYR B 365 PHE 0.023 0.001 PHE D 84 TRP 0.016 0.001 TRP F 36 HIS 0.008 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00460 (35616) covalent geometry : angle 0.58445 (48453) SS BOND : bond 0.00209 ( 47) SS BOND : angle 0.62453 ( 94) hydrogen bonds : bond 0.05334 ( 935) hydrogen bonds : angle 4.61596 ( 2682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 87 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8106 (tm) REVERT: B 151 MET cc_start: 0.4167 (ptt) cc_final: 0.3871 (ptt) REVERT: B 175 MET cc_start: 0.8636 (mpt) cc_final: 0.8275 (mmt) REVERT: B 242 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9014 (tm) REVERT: B 587 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8577 (pp) REVERT: B 1010 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9210 (mp10) REVERT: A 449 TYR cc_start: 0.9083 (t80) cc_final: 0.8572 (m-80) REVERT: E 2 MET cc_start: 0.6746 (tmt) cc_final: 0.6200 (tmt) REVERT: E 67 ARG cc_start: 0.5158 (ppt90) cc_final: 0.4682 (ppt90) REVERT: E 74 MET cc_start: 0.8870 (mmm) cc_final: 0.8290 (mmm) REVERT: G 2 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5446 (ppp) REVERT: I 2 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5358 (ppp) REVERT: I 74 MET cc_start: 0.6502 (mtp) cc_final: 0.6245 (tpp) REVERT: I 81 MET cc_start: -0.2296 (ttp) cc_final: -0.2619 (tmm) REVERT: I 87 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.8381 (ptp90) REVERT: H 80 GLU cc_start: 0.7112 (tp30) cc_final: 0.6516 (mt-10) REVERT: H 166 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7736 (tm-30) REVERT: C 136 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8488 (t80) REVERT: C 151 MET cc_start: 0.7293 (pmm) cc_final: 0.6885 (pmm) REVERT: C 175 MET cc_start: 0.7984 (tmm) cc_final: 0.7618 (ptt) REVERT: C 238 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 697 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9019 (ptm) REVERT: C 811 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8368 (ptpp) outliers start: 68 outliers final: 41 residues processed: 148 average time/residue: 0.6612 time to fit residues: 119.8965 Evaluate side-chains 136 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 246 optimal weight: 7.9990 chunk 387 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 279 optimal weight: 40.0000 chunk 438 optimal weight: 1.9990 chunk 413 optimal weight: 0.5980 chunk 46 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.103751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.059841 restraints weight = 152624.047| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.16 r_work: 0.2888 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35663 Z= 0.102 Angle : 0.538 13.657 48547 Z= 0.271 Chirality : 0.042 0.259 5445 Planarity : 0.003 0.042 6273 Dihedral : 4.094 56.132 4832 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.27 % Rotamer: Outliers : 1.31 % Allowed : 15.37 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 4431 helix: 1.85 (0.22), residues: 661 sheet: -0.29 (0.15), residues: 1193 loop : -2.24 (0.11), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 103 TYR 0.024 0.001 TYR G 80 PHE 0.021 0.001 PHE F 140 TRP 0.023 0.001 TRP F 36 HIS 0.009 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00238 (35616) covalent geometry : angle 0.53777 (48453) SS BOND : bond 0.00183 ( 47) SS BOND : angle 0.53878 ( 94) hydrogen bonds : bond 0.04173 ( 935) hydrogen bonds : angle 4.34147 ( 2682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8862 Ramachandran restraints generated. 4431 Oldfield, 0 Emsley, 4431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8021 (tm) REVERT: B 151 MET cc_start: 0.4229 (ptt) cc_final: 0.3963 (ptt) REVERT: B 175 MET cc_start: 0.8677 (mpt) cc_final: 0.8213 (tpt) REVERT: B 242 LEU cc_start: 0.9248 (mp) cc_final: 0.8920 (tp) REVERT: B 587 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8506 (pp) REVERT: B 1010 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.9187 (mp10) REVERT: A 449 TYR cc_start: 0.9187 (t80) cc_final: 0.8727 (m-80) REVERT: A 568 ASP cc_start: 0.9293 (t0) cc_final: 0.8928 (t70) REVERT: A 740 MET cc_start: 0.9295 (tpt) cc_final: 0.8492 (tmm) REVERT: E 2 MET cc_start: 0.6883 (tmt) cc_final: 0.6336 (tmt) REVERT: E 30 ASP cc_start: 0.9422 (t0) cc_final: 0.9215 (t0) REVERT: E 67 ARG cc_start: 0.5207 (ppt90) cc_final: 0.4646 (ppt90) REVERT: E 74 MET cc_start: 0.8787 (mmm) cc_final: 0.8138 (mmm) REVERT: G 2 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.4814 (ppp) REVERT: I 2 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.4157 (ppp) REVERT: I 74 MET cc_start: 0.6419 (mtp) cc_final: 0.6158 (mmt) REVERT: I 81 MET cc_start: -0.2288 (ttp) cc_final: -0.2617 (tmm) REVERT: I 87 ARG cc_start: 0.8672 (ptm-80) cc_final: 0.8411 (ptp90) REVERT: H 166 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7754 (tm-30) REVERT: C 136 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8403 (t80) REVERT: C 151 MET cc_start: 0.7306 (pmm) cc_final: 0.6870 (pmm) REVERT: C 175 MET cc_start: 0.8018 (tmm) cc_final: 0.7604 (ptm) REVERT: C 697 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.9013 (ptm) REVERT: C 811 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8358 (ptpp) outliers start: 51 outliers final: 33 residues processed: 138 average time/residue: 0.6331 time to fit residues: 107.4973 Evaluate side-chains 133 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain I residue 2 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 86 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 278 optimal weight: 30.0000 chunk 398 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 393 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B 901 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.109752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.070553 restraints weight = 168355.619| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 6.31 r_work: 0.2791 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35663 Z= 0.197 Angle : 0.587 12.920 48547 Z= 0.301 Chirality : 0.043 0.250 5445 Planarity : 0.004 0.042 6273 Dihedral : 4.254 56.004 4832 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.08 % Favored : 91.90 % Rotamer: Outliers : 1.44 % Allowed : 15.27 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 4431 helix: 1.59 (0.22), residues: 669 sheet: -0.37 (0.15), residues: 1230 loop : -2.24 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.026 0.001 TYR B 904 PHE 0.022 0.001 PHE B 136 TRP 0.014 0.001 TRP F 36 HIS 0.008 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00463 (35616) covalent geometry : angle 0.58654 (48453) SS BOND : bond 0.00207 ( 47) SS BOND : angle 0.59873 ( 94) hydrogen bonds : bond 0.05412 ( 935) hydrogen bonds : angle 4.59224 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23512.60 seconds wall clock time: 398 minutes 10.30 seconds (23890.30 seconds total)