Starting phenix.real_space_refine on Fri Mar 6 23:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wd7_32433/03_2026/7wd7_32433.map" } resolution = 3.5 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= 0.006 sd= 0.106 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 156 5.16 5 C 22467 2.51 5 N 5850 2.21 5 O 6849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35322 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 50, 'TRANS': 1022} Chain breaks: 6 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 2, 'PTRANS': 52, 'TRANS': 1024} Chain breaks: 6 Chain: "e" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "f" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1693 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Time building chain proxies: 8.39, per 1000 atoms: 0.24 Number of scatterers: 35322 At special positions: 0 Unit cell: (160.671, 161.764, 281.994, 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 156 16.00 O 6849 8.00 N 5850 7.00 C 22467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 94 " distance=2.03 Simple disulfide: pdb=" SG CYS d 139 " - pdb=" SG CYS d 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 144 " - pdb=" SG CYS e 199 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 94 " distance=2.03 Simple disulfide: pdb=" SG CYS f 139 " - pdb=" SG CYS f 199 " 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: 2.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 77 sheets defined 17.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.555A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.792A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.433A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.653A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.517A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.590A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.955A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.532A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.584A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.951A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.922A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.679A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.429A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.164A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 91 removed outlier: 4.136A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 132 Processing helix chain 'b' and resid 188 through 193 removed outlier: 3.604A pdb=" N GLU b 192 " --> pdb=" O LYS b 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG b 193 " --> pdb=" O ASP b 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 188 through 193' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.592A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.683A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.687A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.683A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.523A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (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 758 through 780 removed outlier: 3.616A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.962A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.570A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.582A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.972A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.627A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.952A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.661A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.441A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.170A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B1156 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 91 removed outlier: 3.965A pdb=" N SER c 91 " --> pdb=" O PHE c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 132 removed outlier: 3.800A pdb=" N LEU d 130 " --> pdb=" O SER d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 193 removed outlier: 3.511A pdb=" N GLU d 192 " --> pdb=" O LYS d 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.603A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.694A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.692A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.504A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.596A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.985A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 854 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.505A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.569A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.970A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.637A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.964A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.683A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.503A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.172A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C1156 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 removed outlier: 3.794A pdb=" N SER e 91 " --> pdb=" O PHE e 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 89 removed outlier: 4.084A pdb=" N LEU f 89 " --> pdb=" O ALA f 86 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 132 removed outlier: 3.792A pdb=" N LEU f 130 " --> pdb=" O SER f 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 193 removed outlier: 3.500A pdb=" N GLU f 192 " --> pdb=" O LYS f 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.199A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.515A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.529A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.523A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.694A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.940A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.793A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.540A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.813A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.538A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.593A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'a' and resid 5 through 6 removed outlier: 3.521A pdb=" N GLU a 82 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP a 57 " --> pdb=" O ASN a 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE a 106 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.916A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 185 " --> pdb=" O LEU a 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER a 184 " --> pdb=" O HIS a 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.916A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 185 " --> pdb=" O LEU a 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.591A pdb=" N THR a 155 " --> pdb=" O ALA a 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN a 200 " --> pdb=" O THR a 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS a 212 " --> pdb=" O CYS a 199 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL a 201 " --> pdb=" O VAL a 210 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL a 210 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR a 208 " --> pdb=" O HIS a 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.729A pdb=" N SER b 7 " --> pdb=" O THR b 22 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 10 through 12 removed outlier: 7.073A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER b 59 " --> pdb=" O TYR b 55 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.744A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 134 through 144 removed outlier: 6.389A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.874A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS b 212 " --> pdb=" O CYS b 199 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA b 201 " --> pdb=" O ILE b 210 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE b 210 " --> pdb=" O ALA b 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.166A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.471A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.514A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.549A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.540A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 325 through 326 removed outlier: 4.966A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 355 through 356 removed outlier: 4.069A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 448 through 453 removed outlier: 7.118A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 495 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 653 through 655 removed outlier: 5.793A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.543A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.570A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'c' and resid 5 through 6 removed outlier: 3.655A pdb=" N VAL c 18 " --> pdb=" O PHE c 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU c 10 " --> pdb=" O THR c 114 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL c 93 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N MET c 34 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU c 10 " --> pdb=" O THR c 114 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.865A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY c 148 " --> pdb=" O TYR c 179 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 124 through 128 removed outlier: 3.865A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY c 148 " --> pdb=" O TYR c 179 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR c 179 " --> pdb=" O GLY c 148 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 155 through 158 removed outlier: 3.922A pdb=" N VAL c 197 " --> pdb=" O ILE c 214 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.646A pdb=" N SER d 7 " --> pdb=" O THR d 22 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 10 through 12 removed outlier: 7.128A pdb=" N LEU d 11 " --> pdb=" O GLU d 111 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP d 41 " --> pdb=" O LEU d 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 30 through 31 removed outlier: 3.745A pdb=" N TYR d 31 " --> pdb=" O LYS d 36 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS d 36 " --> pdb=" O TYR d 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'd' and resid 119 through 123 removed outlier: 3.819A pdb=" N THR d 119 " --> pdb=" O ASN d 142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN d 142 " --> pdb=" O THR d 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER d 121 " --> pdb=" O PHE d 140 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL d 138 " --> pdb=" O PHE d 123 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS d 139 " --> pdb=" O SER d 182 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER d 182 " --> pdb=" O CYS d 139 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR d 178 " --> pdb=" O ASN d 143 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 158 through 159 removed outlier: 3.675A pdb=" N ASN d 150 " --> pdb=" O THR d 202 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR d 197 " --> pdb=" O PHE d 214 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE d 214 " --> pdb=" O TYR d 197 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS d 199 " --> pdb=" O LYS d 212 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS d 212 " --> pdb=" O CYS d 199 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA d 201 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE d 210 " --> pdb=" O ALA d 201 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.167A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.504A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.593A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.527A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.243A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.341A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 448 through 453 removed outlier: 7.096A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 653 through 655 removed outlier: 5.797A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.521A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.611A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AH2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AH3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AH4, first strand: chain 'e' and resid 5 through 6 removed outlier: 3.654A pdb=" N VAL e 18 " --> pdb=" O PHE e 83 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL e 93 " --> pdb=" O GLN e 39 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY e 50 " --> pdb=" O MET e 34 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP e 36 " --> pdb=" O ILE e 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.954A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY e 148 " --> pdb=" O TYR e 179 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 124 through 128 removed outlier: 3.954A pdb=" N GLY e 143 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY e 148 " --> pdb=" O TYR e 179 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR e 179 " --> pdb=" O GLY e 148 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 155 through 158 removed outlier: 3.866A pdb=" N VAL e 197 " --> pdb=" O ILE e 214 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL e 201 " --> pdb=" O VAL e 210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL e 210 " --> pdb=" O VAL e 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR e 208 " --> pdb=" O HIS e 203 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'f' and resid 4 through 7 removed outlier: 3.691A pdb=" N SER f 7 " --> pdb=" O THR f 22 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR f 22 " --> pdb=" O SER f 7 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'f' and resid 10 through 12 removed outlier: 7.172A pdb=" N LEU f 11 " --> pdb=" O GLU f 111 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU f 39 " --> pdb=" O TYR f 55 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR f 55 " --> pdb=" O LEU f 39 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP f 41 " --> pdb=" O LEU f 53 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR f 55 " --> pdb=" O SER f 59 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER f 59 " --> pdb=" O TYR f 55 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 30 through 31 removed outlier: 3.752A pdb=" N TYR f 31 " --> pdb=" O LYS f 36 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS f 36 " --> pdb=" O TYR f 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'f' and resid 119 through 123 removed outlier: 3.824A pdb=" N THR f 119 " --> pdb=" O ASN f 142 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN f 142 " --> pdb=" O THR f 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER f 121 " --> pdb=" O PHE f 140 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL f 138 " --> pdb=" O PHE f 123 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS f 139 " --> pdb=" O SER f 182 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER f 182 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR f 178 " --> pdb=" O ASN f 143 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 158 through 159 removed outlier: 3.702A pdb=" N ASN f 150 " --> pdb=" O THR f 202 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR f 197 " --> pdb=" O PHE f 214 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE f 214 " --> pdb=" O TYR f 197 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS f 199 " --> pdb=" O LYS f 212 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS f 212 " --> pdb=" O CYS f 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA f 201 " --> pdb=" O ILE f 210 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE f 210 " --> pdb=" O ALA f 201 " (cutoff:3.500A) 1221 hydrogen bonds defined for protein. 3312 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: 10.35 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11312 1.34 - 1.46: 8961 1.46 - 1.58: 15685 1.58 - 1.70: 0 1.70 - 1.82: 201 Bond restraints: 36159 Sorted by residual: bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.34e-02 1.83e+03 1.32e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.17e+01 bond pdb=" C LYS B 424 " pdb=" N LEU B 425 " ideal model delta sigma weight residual 1.332 1.391 -0.060 1.92e-02 2.71e+03 9.65e+00 bond pdb=" CA CYS C 336 " pdb=" C CYS C 336 " ideal model delta sigma weight residual 1.524 1.560 -0.036 1.26e-02 6.30e+03 8.24e+00 bond pdb=" C LYS C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.332 1.386 -0.054 1.92e-02 2.71e+03 7.98e+00 ... (remaining 36154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 49110 3.48 - 6.96: 99 6.96 - 10.43: 2 10.43 - 13.91: 1 13.91 - 17.39: 3 Bond angle restraints: 49215 Sorted by residual: angle pdb=" N LEU C 335 " pdb=" CA LEU C 335 " pdb=" C LEU C 335 " ideal model delta sigma weight residual 110.30 125.46 -15.16 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 127.00 144.39 -17.39 2.40e+00 1.74e-01 5.25e+01 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CD PRO B 330 " ideal model delta sigma weight residual 120.60 105.09 15.51 2.20e+00 2.07e-01 4.97e+01 angle pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" C PHE B 329 " ideal model delta sigma weight residual 108.82 120.09 -11.27 1.65e+00 3.67e-01 4.67e+01 angle pdb=" N SER B 530 " pdb=" CA SER B 530 " pdb=" C SER B 530 " ideal model delta sigma weight residual 108.75 117.15 -8.40 1.71e+00 3.42e-01 2.41e+01 ... (remaining 49210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 21327 25.85 - 51.70: 172 51.70 - 77.55: 24 77.55 - 103.41: 22 103.41 - 129.26: 1 Dihedral angle restraints: 21546 sinusoidal: 8334 harmonic: 13212 Sorted by residual: dihedral pdb=" CA LEU C 335 " pdb=" C LEU C 335 " pdb=" N CYS C 336 " pdb=" CA CYS C 336 " ideal model delta harmonic sigma weight residual -180.00 -50.74 -129.26 0 5.00e+00 4.00e-02 6.68e+02 dihedral pdb=" CA CYS B 291 " pdb=" C CYS B 291 " pdb=" N ALA B 292 " pdb=" CA ALA B 292 " ideal model delta harmonic sigma weight residual 180.00 126.26 53.74 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA CYS C 291 " pdb=" C CYS C 291 " pdb=" N ALA C 292 " pdb=" CA ALA C 292 " ideal model delta harmonic sigma weight residual 180.00 126.41 53.59 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 21543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4677 0.054 - 0.108: 739 0.108 - 0.162: 137 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 5556 Sorted by residual: chirality pdb=" CA LEU C 335 " pdb=" N LEU C 335 " pdb=" C LEU C 335 " pdb=" CB LEU C 335 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA ALA b 114 " pdb=" N ALA b 114 " pdb=" C ALA b 114 " pdb=" CB ALA b 114 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 5553 not shown) Planarity restraints: 6348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO C 337 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 117 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA a 117 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA a 117 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA a 118 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 291 " 0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C CYS A 291 " -0.075 2.00e-02 2.50e+03 pdb=" O CYS A 291 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 292 " 0.025 2.00e-02 2.50e+03 ... (remaining 6345 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1030 2.71 - 3.25: 32574 3.25 - 3.80: 52693 3.80 - 4.35: 67017 4.35 - 4.90: 114177 Nonbonded interactions: 267491 Sorted by model distance: nonbonded pdb=" O ASN C 448 " pdb=" OG SER C 494 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR b 42 " pdb=" OE1 GLN b 95 " model vdw 2.158 3.040 nonbonded pdb=" O ASN B 448 " pdb=" OG SER B 494 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" NE2 GLN A1106 " model vdw 2.232 3.120 nonbonded pdb=" O GLY A 215 " pdb=" OH TYR A 266 " model vdw 2.238 3.040 ... (remaining 267486 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 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.210 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: 0.060 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.360 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 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 : 0.002 0.085 36208 Z= 0.139 Angle : 0.602 17.389 49313 Z= 0.365 Chirality : 0.042 0.271 5556 Planarity : 0.004 0.110 6348 Dihedral : 8.226 129.257 12903 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.03 % Allowed : 0.18 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.14 % 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: -1.98 (0.10), residues: 4476 helix: -2.88 (0.12), residues: 650 sheet: -0.19 (0.14), residues: 1129 loop : -1.42 (0.10), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 328 TYR 0.015 0.001 TYR C 145 PHE 0.017 0.001 PHE B 329 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS d 203 Details of bonding type rmsd covalent geometry : bond 0.00232 (36159) covalent geometry : angle 0.60079 (49215) SS BOND : bond 0.00229 ( 49) SS BOND : angle 1.06307 ( 98) hydrogen bonds : bond 0.30054 ( 1174) hydrogen bonds : angle 10.07916 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 916 time to evaluate : 1.254 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.1350 (m-70) cc_final: -0.3110 (p-80) REVERT: A 177 MET cc_start: 0.0269 (ttm) cc_final: -0.0170 (mtm) REVERT: A 203 ILE cc_start: 0.8192 (mt) cc_final: 0.7948 (mt) REVERT: A 387 LEU cc_start: 0.7780 (tp) cc_final: 0.7529 (tp) REVERT: A 462 LYS cc_start: 0.7463 (mttt) cc_final: 0.7173 (pttp) REVERT: A 693 ILE cc_start: 0.8200 (pt) cc_final: 0.7980 (pt) REVERT: A 979 ASP cc_start: 0.6730 (t0) cc_final: 0.6368 (t0) REVERT: a 98 ARG cc_start: 0.3755 (ttp80) cc_final: 0.2468 (mmp80) REVERT: b 211 VAL cc_start: 0.3175 (m) cc_final: 0.2558 (p) REVERT: B 608 VAL cc_start: 0.8839 (t) cc_final: 0.8616 (m) REVERT: B 858 LEU cc_start: 0.8188 (mt) cc_final: 0.7988 (mt) REVERT: d 4 MET cc_start: -0.0387 (mtm) cc_final: -0.3263 (ppp) REVERT: C 357 ARG cc_start: 0.4801 (ttm-80) cc_final: 0.4469 (tpm170) REVERT: C 588 THR cc_start: 0.8603 (m) cc_final: 0.8326 (p) REVERT: e 127 PRO cc_start: 0.0326 (Cg_endo) cc_final: -0.0191 (Cg_exo) REVERT: f 4 MET cc_start: -0.0010 (mtm) cc_final: -0.2149 (ptm) outliers start: 1 outliers final: 0 residues processed: 917 average time/residue: 0.2047 time to fit residues: 303.6468 Evaluate side-chains 418 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 0.4980 chunk 424 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 61 ASN A 644 GLN A 787 GLN A 901 GLN A1010 GLN A1106 GLN A1159 HIS a 3 GLN a 168 HIS b 171 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 388 ASN B 506 GLN B 641 ASN B 787 GLN B 901 GLN B 955 ASN B1010 GLN B1048 HIS B1088 HIS B1106 GLN B1159 HIS d 96 GLN ** d 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 334 ASN C 506 GLN C 580 GLN C 655 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 935 GLN C 955 ASN C1048 HIS C1088 HIS C1159 HIS e 41 HIS e 61 ASN e 168 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.183648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.145913 restraints weight = 107985.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.145500 restraints weight = 67613.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.146995 restraints weight = 41809.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.147084 restraints weight = 27074.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.147401 restraints weight = 27028.796| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 36208 Z= 0.138 Angle : 0.619 10.577 49313 Z= 0.322 Chirality : 0.045 0.216 5556 Planarity : 0.005 0.094 6348 Dihedral : 4.392 72.858 4854 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 2.14 % Allowed : 8.31 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.21 % Twisted Proline : 0.44 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.11), residues: 4476 helix: 0.31 (0.19), residues: 641 sheet: 0.28 (0.13), residues: 1150 loop : -1.19 (0.10), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 102 TYR 0.023 0.001 TYR b 55 PHE 0.025 0.002 PHE d 214 TRP 0.015 0.001 TRP C 886 HIS 0.009 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00302 (36159) covalent geometry : angle 0.61527 (49215) SS BOND : bond 0.00926 ( 49) SS BOND : angle 1.61178 ( 98) hydrogen bonds : bond 0.05176 ( 1174) hydrogen bonds : angle 6.38722 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 469 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.1117 (m-70) cc_final: -0.3379 (p-80) REVERT: A 177 MET cc_start: 0.3140 (ttm) cc_final: 0.2108 (ptp) REVERT: A 462 LYS cc_start: 0.7495 (mttt) cc_final: 0.7246 (pttp) REVERT: A 571 ASP cc_start: 0.7179 (t70) cc_final: 0.6802 (t0) REVERT: a 98 ARG cc_start: 0.3114 (ttp80) cc_final: 0.2852 (mmp80) REVERT: B 177 MET cc_start: 0.3842 (OUTLIER) cc_final: 0.2844 (mtm) REVERT: B 858 LEU cc_start: 0.8413 (mt) cc_final: 0.8150 (mt) REVERT: B 970 PHE cc_start: 0.8536 (m-80) cc_final: 0.8282 (m-80) REVERT: B 1092 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7034 (mt-10) REVERT: c 81 MET cc_start: -0.3585 (ttt) cc_final: -0.4469 (ptm) REVERT: d 4 MET cc_start: 0.1918 (mtm) cc_final: 0.0978 (mpp) REVERT: C 357 ARG cc_start: 0.5898 (ttm-80) cc_final: 0.4474 (tpm170) REVERT: C 588 THR cc_start: 0.9033 (m) cc_final: 0.8751 (p) REVERT: C 817 PHE cc_start: 0.8451 (t80) cc_final: 0.7879 (t80) REVERT: C 1019 ARG cc_start: 0.8169 (tpt170) cc_final: 0.7779 (ttp80) REVERT: e 34 MET cc_start: 0.2577 (mpp) cc_final: 0.2326 (tpp) REVERT: f 4 MET cc_start: 0.2026 (mtm) cc_final: -0.1582 (ptm) outliers start: 85 outliers final: 45 residues processed: 524 average time/residue: 0.1902 time to fit residues: 167.3263 Evaluate side-chains 385 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain d residue 196 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 76 ASP Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 72 optimal weight: 0.7980 chunk 212 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 180 optimal weight: 0.0970 chunk 432 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 362 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 146 HIS A 498 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 194 HIS B 146 HIS B 409 GLN B 563 GLN B 641 ASN B1005 GLN d 44 GLN d 171 GLN C 146 HIS C 334 ASN C 506 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.180997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.144612 restraints weight = 108263.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.143473 restraints weight = 80496.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.144276 restraints weight = 46405.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.144611 restraints weight = 35668.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144696 restraints weight = 30983.882| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36208 Z= 0.116 Angle : 0.557 10.410 49313 Z= 0.288 Chirality : 0.043 0.180 5556 Planarity : 0.004 0.086 6348 Dihedral : 4.228 56.268 4854 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 1.86 % Allowed : 10.07 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.21 % Twisted Proline : 0.44 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 4476 helix: 1.18 (0.20), residues: 654 sheet: 0.47 (0.14), residues: 1183 loop : -1.00 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.023 0.001 TYR C 508 PHE 0.026 0.001 PHE C 643 TRP 0.019 0.001 TRP d 168 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00253 (36159) covalent geometry : angle 0.55468 (49215) SS BOND : bond 0.00319 ( 49) SS BOND : angle 1.23224 ( 98) hydrogen bonds : bond 0.04217 ( 1174) hydrogen bonds : angle 5.59427 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 381 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0997 (m90) cc_final: -0.3270 (p-80) REVERT: A 177 MET cc_start: 0.2513 (ttm) cc_final: 0.0668 (ptm) REVERT: A 462 LYS cc_start: 0.7565 (mttt) cc_final: 0.7137 (pttp) REVERT: A 571 ASP cc_start: 0.7273 (t70) cc_final: 0.6970 (t0) REVERT: A 817 PHE cc_start: 0.8259 (t80) cc_final: 0.8046 (t80) REVERT: A 979 ASP cc_start: 0.7128 (t0) cc_final: 0.6806 (t0) REVERT: a 34 MET cc_start: 0.2934 (ptp) cc_final: 0.2596 (ptm) REVERT: a 81 MET cc_start: 0.1148 (ppp) cc_final: -0.0539 (tmm) REVERT: a 98 ARG cc_start: 0.4088 (ttp80) cc_final: 0.3048 (mmp80) REVERT: B 140 PHE cc_start: 0.4108 (OUTLIER) cc_final: 0.3722 (m-80) REVERT: B 327 VAL cc_start: 0.7767 (m) cc_final: 0.7434 (p) REVERT: B 457 ARG cc_start: 0.3214 (mtp-110) cc_final: 0.2767 (ptp-110) REVERT: B 858 LEU cc_start: 0.8310 (mt) cc_final: 0.8056 (mt) REVERT: B 970 PHE cc_start: 0.8584 (m-80) cc_final: 0.8264 (m-80) REVERT: c 81 MET cc_start: -0.3672 (ttt) cc_final: -0.4228 (ptm) REVERT: d 4 MET cc_start: 0.1505 (mtm) cc_final: 0.0667 (mpp) REVERT: C 357 ARG cc_start: 0.5848 (ttm-80) cc_final: 0.5446 (mmm160) REVERT: C 423 TYR cc_start: 0.3194 (t80) cc_final: 0.2967 (t80) REVERT: C 588 THR cc_start: 0.8941 (m) cc_final: 0.8681 (p) REVERT: C 817 PHE cc_start: 0.8578 (t80) cc_final: 0.7901 (t80) REVERT: C 1019 ARG cc_start: 0.8205 (tpt170) cc_final: 0.7763 (ttp80) REVERT: f 4 MET cc_start: 0.2193 (mtm) cc_final: -0.1639 (ttp) outliers start: 74 outliers final: 46 residues processed: 434 average time/residue: 0.1855 time to fit residues: 135.8172 Evaluate side-chains 356 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain f residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 12 optimal weight: 0.0270 chunk 439 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 35 optimal weight: 0.0050 chunk 76 optimal weight: 0.4980 chunk 136 optimal weight: 8.9990 chunk 425 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 25 optimal weight: 0.2980 chunk 262 optimal weight: 3.9990 overall best weight: 0.2652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 751 ASN A1010 GLN A1119 ASN B 99 ASN B 388 ASN d 95 GLN C 613 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.181569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.143895 restraints weight = 107933.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.143355 restraints weight = 69148.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.143674 restraints weight = 46265.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.144085 restraints weight = 35375.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144243 restraints weight = 28700.474| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36208 Z= 0.099 Angle : 0.529 11.039 49313 Z= 0.273 Chirality : 0.042 0.178 5556 Planarity : 0.004 0.082 6348 Dihedral : 4.124 49.385 4854 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 1.84 % Allowed : 10.70 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 4476 helix: 1.59 (0.20), residues: 659 sheet: 0.55 (0.14), residues: 1195 loop : -0.90 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.023 0.001 TYR f 93 PHE 0.026 0.001 PHE f 77 TRP 0.025 0.001 TRP c 107 HIS 0.005 0.000 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00212 (36159) covalent geometry : angle 0.52784 (49215) SS BOND : bond 0.00307 ( 49) SS BOND : angle 0.93898 ( 98) hydrogen bonds : bond 0.03688 ( 1174) hydrogen bonds : angle 5.24762 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 1.035 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: A 146 HIS cc_start: -0.0741 (m90) cc_final: -0.3211 (p-80) REVERT: A 177 MET cc_start: 0.2706 (ttm) cc_final: 0.1775 (ttp) REVERT: A 462 LYS cc_start: 0.7724 (mttt) cc_final: 0.7209 (pttp) REVERT: A 571 ASP cc_start: 0.7292 (t70) cc_final: 0.6854 (t0) REVERT: A 979 ASP cc_start: 0.7256 (t0) cc_final: 0.7043 (t0) REVERT: a 81 MET cc_start: 0.1273 (ppp) cc_final: 0.1037 (tmm) REVERT: a 89 ASP cc_start: 0.3328 (p0) cc_final: 0.2689 (t70) REVERT: B 140 PHE cc_start: 0.4028 (OUTLIER) cc_final: 0.3653 (m-80) REVERT: B 457 ARG cc_start: 0.3402 (mtp-110) cc_final: 0.2787 (ptp-110) REVERT: B 858 LEU cc_start: 0.8261 (mt) cc_final: 0.8021 (mt) REVERT: B 970 PHE cc_start: 0.8578 (m-80) cc_final: 0.8264 (m-80) REVERT: c 32 TYR cc_start: 0.4743 (m-80) cc_final: 0.4486 (m-80) REVERT: c 98 ARG cc_start: 0.0596 (tpt-90) cc_final: 0.0295 (mmt180) REVERT: d 4 MET cc_start: 0.1737 (mtm) cc_final: 0.0823 (mpp) REVERT: d 186 LEU cc_start: 0.3719 (OUTLIER) cc_final: 0.3403 (mt) REVERT: C 198 ASP cc_start: 0.6763 (t0) cc_final: 0.6353 (p0) REVERT: C 357 ARG cc_start: 0.5923 (ttm-80) cc_final: 0.5525 (mmm160) REVERT: C 423 TYR cc_start: 0.3313 (t80) cc_final: 0.3054 (t80) REVERT: C 588 THR cc_start: 0.8929 (m) cc_final: 0.8624 (p) REVERT: C 817 PHE cc_start: 0.8566 (t80) cc_final: 0.7958 (t80) REVERT: C 1019 ARG cc_start: 0.8290 (tpt170) cc_final: 0.7783 (ttp80) REVERT: f 4 MET cc_start: 0.2275 (mtm) cc_final: -0.1532 (ttp) outliers start: 73 outliers final: 41 residues processed: 412 average time/residue: 0.1868 time to fit residues: 130.1976 Evaluate side-chains 355 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain f residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 87 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.0270 chunk 403 optimal weight: 1.9990 chunk 240 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 422 optimal weight: 1.9990 chunk 355 optimal weight: 0.2980 chunk 306 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 69 HIS a 3 GLN B 955 ASN d 96 GLN C 409 GLN C 774 GLN C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.179211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.142050 restraints weight = 107077.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.141387 restraints weight = 83975.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.141845 restraints weight = 46992.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.141825 restraints weight = 42362.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.142101 restraints weight = 35687.075| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36208 Z= 0.118 Angle : 0.534 8.185 49313 Z= 0.277 Chirality : 0.043 0.169 5556 Planarity : 0.004 0.076 6348 Dihedral : 4.130 42.024 4854 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 2.39 % Allowed : 10.65 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4476 helix: 1.70 (0.20), residues: 682 sheet: 0.47 (0.14), residues: 1237 loop : -0.80 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.025 0.001 TYR f 55 PHE 0.020 0.001 PHE A 906 TRP 0.044 0.002 TRP f 56 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00267 (36159) covalent geometry : angle 0.53297 (49215) SS BOND : bond 0.00557 ( 49) SS BOND : angle 0.92705 ( 98) hydrogen bonds : bond 0.03639 ( 1174) hydrogen bonds : angle 4.97132 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 348 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: -0.0994 (OUTLIER) cc_final: -0.1199 (tt) REVERT: A 146 HIS cc_start: -0.0318 (m90) cc_final: -0.3213 (p-80) REVERT: A 177 MET cc_start: 0.2867 (ttm) cc_final: 0.2004 (ttm) REVERT: A 571 ASP cc_start: 0.7398 (t70) cc_final: 0.6910 (t0) REVERT: A 858 LEU cc_start: 0.8457 (mm) cc_final: 0.8171 (mm) REVERT: A 979 ASP cc_start: 0.7196 (t0) cc_final: 0.6991 (t0) REVERT: B 140 PHE cc_start: 0.3772 (OUTLIER) cc_final: 0.2938 (m-80) REVERT: B 327 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7290 (p) REVERT: B 457 ARG cc_start: 0.2963 (mtp-110) cc_final: 0.2250 (ptp-110) REVERT: B 970 PHE cc_start: 0.8548 (m-80) cc_final: 0.8217 (m-80) REVERT: B 1031 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: c 98 ARG cc_start: 0.0889 (tpt-90) cc_final: 0.0490 (mmt180) REVERT: d 4 MET cc_start: 0.1431 (mtm) cc_final: -0.0085 (mpp) REVERT: d 186 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3413 (mt) REVERT: C 198 ASP cc_start: 0.6544 (t0) cc_final: 0.6317 (p0) REVERT: C 423 TYR cc_start: 0.3218 (t80) cc_final: 0.2736 (t80) REVERT: C 588 THR cc_start: 0.8977 (m) cc_final: 0.8744 (p) REVERT: C 730 SER cc_start: 0.9272 (t) cc_final: 0.8866 (p) REVERT: C 817 PHE cc_start: 0.8597 (t80) cc_final: 0.7876 (t80) REVERT: C 1031 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: f 4 MET cc_start: 0.2422 (mtm) cc_final: -0.1365 (ttp) outliers start: 95 outliers final: 65 residues processed: 423 average time/residue: 0.1889 time to fit residues: 136.0796 Evaluate side-chains 370 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 299 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 49 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 68 optimal weight: 0.0000 chunk 294 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1119 ASN a 135 GLN B1088 HIS d 34 ASN C 641 ASN C 655 HIS C 762 GLN C1101 HIS e 61 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.176458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.140572 restraints weight = 105119.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.138097 restraints weight = 86959.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.138711 restraints weight = 55299.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.139213 restraints weight = 40908.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.139349 restraints weight = 35213.692| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36208 Z= 0.155 Angle : 0.585 7.965 49313 Z= 0.304 Chirality : 0.044 0.199 5556 Planarity : 0.004 0.068 6348 Dihedral : 4.424 42.400 4854 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 2.64 % Allowed : 11.20 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4476 helix: 1.51 (0.20), residues: 696 sheet: 0.47 (0.14), residues: 1279 loop : -0.81 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 466 TYR 0.023 0.002 TYR f 38 PHE 0.021 0.002 PHE B 906 TRP 0.044 0.002 TRP A 886 HIS 0.006 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00356 (36159) covalent geometry : angle 0.58366 (49215) SS BOND : bond 0.00555 ( 49) SS BOND : angle 1.15635 ( 98) hydrogen bonds : bond 0.03931 ( 1174) hydrogen bonds : angle 5.07951 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 330 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0139 (m90) cc_final: -0.2239 (p-80) REVERT: A 177 MET cc_start: 0.2775 (ttm) cc_final: 0.1959 (ttm) REVERT: A 571 ASP cc_start: 0.7351 (t70) cc_final: 0.6875 (t0) REVERT: A 817 PHE cc_start: 0.8380 (t80) cc_final: 0.8140 (t80) REVERT: A 914 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8347 (p0) REVERT: A 918 GLU cc_start: 0.7419 (mp0) cc_final: 0.7175 (mp0) REVERT: B 140 PHE cc_start: 0.4032 (OUTLIER) cc_final: 0.3002 (m-80) REVERT: B 737 ASP cc_start: 0.8068 (t0) cc_final: 0.7786 (t70) REVERT: B 1031 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: c 34 MET cc_start: 0.1420 (ppp) cc_final: -0.0112 (ppp) REVERT: c 98 ARG cc_start: 0.0798 (tpt-90) cc_final: 0.0379 (mmt180) REVERT: d 4 MET cc_start: 0.1108 (mtm) cc_final: -0.0205 (mpp) REVERT: d 186 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.3317 (mt) REVERT: C 336 CYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2732 (p) REVERT: C 423 TYR cc_start: 0.3055 (t80) cc_final: 0.2651 (t80) REVERT: C 613 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 730 SER cc_start: 0.9330 (t) cc_final: 0.9104 (p) REVERT: C 780 GLU cc_start: 0.8154 (tt0) cc_final: 0.7940 (tt0) REVERT: C 1019 ARG cc_start: 0.8327 (tpt170) cc_final: 0.7953 (ttp80) REVERT: C 1031 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: f 4 MET cc_start: 0.2515 (mtm) cc_final: -0.1287 (ttp) REVERT: f 184 LEU cc_start: 0.2306 (OUTLIER) cc_final: 0.2066 (mt) outliers start: 105 outliers final: 83 residues processed: 409 average time/residue: 0.1848 time to fit residues: 130.1573 Evaluate side-chains 386 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 295 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 186 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 20 THR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 387 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 429 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 69 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B1011 GLN c 39 GLN d 203 HIS C 99 ASN C 506 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** f 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.171946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.137051 restraints weight = 104759.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134646 restraints weight = 83018.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135041 restraints weight = 56774.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.135458 restraints weight = 46071.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135558 restraints weight = 40579.248| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 36208 Z= 0.205 Angle : 0.671 10.284 49313 Z= 0.349 Chirality : 0.046 0.204 5556 Planarity : 0.005 0.069 6348 Dihedral : 5.024 43.285 4854 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 2.95 % Allowed : 11.93 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4476 helix: 1.31 (0.20), residues: 691 sheet: 0.24 (0.14), residues: 1285 loop : -0.99 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.034 0.002 TYR A 369 PHE 0.032 0.002 PHE C 168 TRP 0.072 0.003 TRP A 886 HIS 0.008 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00478 (36159) covalent geometry : angle 0.66734 (49215) SS BOND : bond 0.00393 ( 49) SS BOND : angle 1.78575 ( 98) hydrogen bonds : bond 0.04401 ( 1174) hydrogen bonds : angle 5.34406 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 333 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.0116 (m90) cc_final: -0.2873 (p90) REVERT: A 571 ASP cc_start: 0.7368 (t70) cc_final: 0.7094 (t0) REVERT: a 81 MET cc_start: 0.0857 (ppp) cc_final: -0.0337 (ppp) REVERT: a 209 LYS cc_start: 0.3550 (mttm) cc_final: 0.3229 (tttm) REVERT: B 64 TRP cc_start: 0.7322 (t60) cc_final: 0.6818 (t60) REVERT: B 140 PHE cc_start: 0.4102 (OUTLIER) cc_final: 0.2790 (m-80) REVERT: B 210 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6934 (tp) REVERT: B 233 ILE cc_start: 0.7721 (mp) cc_final: 0.7367 (mt) REVERT: B 319 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7332 (mtp85) REVERT: B 457 ARG cc_start: 0.2591 (mtp-110) cc_final: 0.2075 (ptp-110) REVERT: B 596 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8581 (p) REVERT: B 737 ASP cc_start: 0.8065 (t0) cc_final: 0.7559 (t70) REVERT: B 1031 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: B 1041 ASP cc_start: 0.7852 (t0) cc_final: 0.7594 (t0) REVERT: B 1144 GLU cc_start: 0.7707 (tp30) cc_final: 0.7404 (tm-30) REVERT: d 4 MET cc_start: 0.0568 (mtm) cc_final: -0.0206 (mpp) REVERT: C 336 CYS cc_start: 0.3136 (OUTLIER) cc_final: 0.2740 (p) REVERT: C 613 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: C 884 SER cc_start: 0.9127 (m) cc_final: 0.8758 (p) REVERT: C 1031 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: C 1142 GLN cc_start: 0.7270 (tp40) cc_final: 0.6974 (tm-30) REVERT: f 4 MET cc_start: 0.2489 (mtm) cc_final: -0.1203 (ptm) outliers start: 117 outliers final: 87 residues processed: 417 average time/residue: 0.1871 time to fit residues: 131.7538 Evaluate side-chains 376 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 282 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 430 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN B 954 GLN c 43 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN e 39 GLN f 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.172033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.136841 restraints weight = 104405.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.134497 restraints weight = 82036.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.134910 restraints weight = 55597.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135127 restraints weight = 45631.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135341 restraints weight = 41398.547| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36208 Z= 0.154 Angle : 0.594 10.030 49313 Z= 0.308 Chirality : 0.044 0.210 5556 Planarity : 0.004 0.086 6348 Dihedral : 4.778 44.262 4854 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 2.44 % Allowed : 12.94 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4476 helix: 1.56 (0.20), residues: 682 sheet: 0.19 (0.14), residues: 1289 loop : -0.95 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.022 0.001 TYR A 904 PHE 0.021 0.002 PHE B 329 TRP 0.047 0.002 TRP A 886 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00357 (36159) covalent geometry : angle 0.59127 (49215) SS BOND : bond 0.00315 ( 49) SS BOND : angle 1.38976 ( 98) hydrogen bonds : bond 0.03937 ( 1174) hydrogen bonds : angle 5.17097 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 298 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: -0.0065 (m90) cc_final: -0.3077 (p-80) REVERT: A 571 ASP cc_start: 0.7479 (t70) cc_final: 0.7266 (t0) REVERT: A 707 TYR cc_start: 0.8237 (t80) cc_final: 0.8017 (t80) REVERT: A 878 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8764 (tt) REVERT: a 81 MET cc_start: 0.0675 (ppp) cc_final: -0.0395 (ppp) REVERT: a 209 LYS cc_start: 0.3531 (mttm) cc_final: 0.3207 (tttm) REVERT: B 140 PHE cc_start: 0.4088 (OUTLIER) cc_final: 0.2834 (m-80) REVERT: B 233 ILE cc_start: 0.7835 (mp) cc_final: 0.7546 (mt) REVERT: B 515 PHE cc_start: 0.5542 (m-10) cc_final: 0.5246 (m-80) REVERT: B 596 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8515 (p) REVERT: B 736 VAL cc_start: 0.8663 (t) cc_final: 0.8421 (m) REVERT: B 737 ASP cc_start: 0.8125 (t0) cc_final: 0.7464 (t70) REVERT: B 1031 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: c 98 ARG cc_start: 0.0844 (tpt-90) cc_final: -0.0082 (mmm-85) REVERT: d 4 MET cc_start: 0.0964 (mtm) cc_final: 0.0324 (mpp) REVERT: C 613 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: C 773 GLU cc_start: 0.7658 (tt0) cc_final: 0.7380 (tt0) REVERT: C 804 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7731 (mm110) REVERT: C 817 PHE cc_start: 0.8621 (t80) cc_final: 0.8159 (t80) REVERT: C 884 SER cc_start: 0.9093 (m) cc_final: 0.8708 (p) REVERT: C 955 ASN cc_start: 0.8793 (t0) cc_final: 0.7989 (m-40) REVERT: C 1019 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7481 (ttp80) REVERT: C 1031 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: e 66 ASP cc_start: 0.5663 (p0) cc_final: 0.5329 (t0) REVERT: f 4 MET cc_start: 0.1907 (mtm) cc_final: -0.1641 (ptm) outliers start: 97 outliers final: 76 residues processed: 370 average time/residue: 0.1840 time to fit residues: 116.0417 Evaluate side-chains 360 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 119 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN a 168 HIS b 95 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN C 188 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1088 HIS e 52 ASN e 175 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.136996 restraints weight = 111708.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137169 restraints weight = 93434.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.137065 restraints weight = 64402.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.137104 restraints weight = 60417.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.137319 restraints weight = 51258.832| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 36208 Z= 0.251 Angle : 0.739 11.006 49313 Z= 0.384 Chirality : 0.048 0.190 5556 Planarity : 0.005 0.124 6348 Dihedral : 5.443 47.870 4854 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.79 % Allowed : 12.74 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.12), residues: 4476 helix: 1.19 (0.20), residues: 690 sheet: -0.25 (0.14), residues: 1300 loop : -1.19 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.043 0.002 TYR C 904 PHE 0.032 0.003 PHE B1148 TRP 0.055 0.003 TRP A 886 HIS 0.014 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00584 (36159) covalent geometry : angle 0.73508 (49215) SS BOND : bond 0.00548 ( 49) SS BOND : angle 1.81033 ( 98) hydrogen bonds : bond 0.04759 ( 1174) hydrogen bonds : angle 5.64647 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 312 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.0116 (m90) cc_final: -0.3279 (p-80) REVERT: a 209 LYS cc_start: 0.3778 (mttm) cc_final: 0.3308 (tttm) REVERT: b 50 PRO cc_start: 0.2300 (Cg_exo) cc_final: 0.2077 (Cg_endo) REVERT: B 64 TRP cc_start: 0.7363 (t60) cc_final: 0.6797 (t60) REVERT: B 140 PHE cc_start: 0.3223 (OUTLIER) cc_final: 0.1909 (m-80) REVERT: B 436 TRP cc_start: 0.2446 (p90) cc_final: 0.1824 (p90) REVERT: B 509 ARG cc_start: 0.2856 (OUTLIER) cc_final: 0.0146 (mtm180) REVERT: B 515 PHE cc_start: 0.5688 (m-10) cc_final: 0.5340 (m-80) REVERT: B 596 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8751 (p) REVERT: B 737 ASP cc_start: 0.7952 (t0) cc_final: 0.7452 (t70) REVERT: B 1031 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: c 23 LYS cc_start: 0.5577 (mtpt) cc_final: 0.5269 (tptm) REVERT: d 4 MET cc_start: 0.1060 (mtm) cc_final: 0.0301 (mpp) REVERT: C 153 MET cc_start: 0.2154 (ppp) cc_final: 0.0931 (mtp) REVERT: C 613 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: C 884 SER cc_start: 0.9040 (m) cc_final: 0.8745 (p) REVERT: C 1031 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: e 66 ASP cc_start: 0.5864 (p0) cc_final: 0.5320 (t0) REVERT: f 174 LYS cc_start: 0.2080 (mmtt) cc_final: 0.1738 (mtpt) outliers start: 111 outliers final: 88 residues processed: 395 average time/residue: 0.1873 time to fit residues: 125.1144 Evaluate side-chains 368 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 274 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain d residue 78 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain e residue 75 SER Chi-restraints excluded: chain e residue 87 THR Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 412 optimal weight: 0.0470 chunk 320 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 348 optimal weight: 0.0770 chunk 254 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 443 optimal weight: 0.0040 chunk 399 optimal weight: 0.6980 chunk 426 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.2848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 69 HIS A 872 GLN B 14 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN C 188 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN e 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.174335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139978 restraints weight = 103442.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137536 restraints weight = 82133.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.137643 restraints weight = 67498.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.137738 restraints weight = 61037.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.138202 restraints weight = 44339.825| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.088 36208 Z= 0.112 Angle : 0.588 11.399 49313 Z= 0.303 Chirality : 0.043 0.194 5556 Planarity : 0.004 0.120 6348 Dihedral : 4.747 46.363 4854 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.54 % Allowed : 14.38 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4476 helix: 1.75 (0.20), residues: 673 sheet: 0.08 (0.14), residues: 1229 loop : -1.02 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.030 0.001 TYR C 904 PHE 0.026 0.001 PHE B 329 TRP 0.038 0.002 TRP B 886 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00246 (36159) covalent geometry : angle 0.58524 (49215) SS BOND : bond 0.00320 ( 49) SS BOND : angle 1.30503 ( 98) hydrogen bonds : bond 0.03602 ( 1174) hydrogen bonds : angle 5.12803 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8952 Ramachandran restraints generated. 4476 Oldfield, 0 Emsley, 4476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8694 (mt) cc_final: 0.8482 (mt) REVERT: A 146 HIS cc_start: -0.0217 (m90) cc_final: -0.3122 (p-80) REVERT: A 1002 GLN cc_start: 0.7848 (tp40) cc_final: 0.7642 (tp40) REVERT: A 1045 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7822 (tptm) REVERT: a 209 LYS cc_start: 0.3390 (mttm) cc_final: 0.3080 (tttm) REVERT: B 140 PHE cc_start: 0.4393 (OUTLIER) cc_final: 0.3111 (m-80) REVERT: B 210 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7126 (tp) REVERT: B 509 ARG cc_start: 0.2738 (OUTLIER) cc_final: 0.0204 (mtm180) REVERT: B 515 PHE cc_start: 0.5611 (m-10) cc_final: 0.5212 (m-80) REVERT: B 737 ASP cc_start: 0.8130 (t0) cc_final: 0.7450 (t70) REVERT: B 751 ASN cc_start: 0.8377 (t0) cc_final: 0.8016 (t0) REVERT: B 1031 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: d 4 MET cc_start: 0.0533 (mtm) cc_final: -0.0055 (mpp) REVERT: C 231 ILE cc_start: 0.8270 (mp) cc_final: 0.7903 (mm) REVERT: C 613 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: C 804 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7689 (mm110) REVERT: C 817 PHE cc_start: 0.8502 (t80) cc_final: 0.8179 (t80) REVERT: C 884 SER cc_start: 0.8877 (m) cc_final: 0.8473 (p) REVERT: C 904 TYR cc_start: 0.7107 (t80) cc_final: 0.6883 (t80) REVERT: C 955 ASN cc_start: 0.8813 (t0) cc_final: 0.7986 (m-40) REVERT: C 1019 ARG cc_start: 0.8332 (tpt170) cc_final: 0.7583 (ttp80) REVERT: C 1031 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: f 4 MET cc_start: 0.1554 (mtt) cc_final: -0.1602 (ptm) outliers start: 61 outliers final: 48 residues processed: 371 average time/residue: 0.1859 time to fit residues: 116.6703 Evaluate side-chains 336 residues out of total 3972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain a residue 144 CYS Chi-restraints excluded: chain a residue 174 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1148 PHE Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 42 TYR Chi-restraints excluded: chain f residue 49 SER Chi-restraints excluded: chain f residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 207 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 430 optimal weight: 0.0270 chunk 176 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN C 14 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.169437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.134136 restraints weight = 102487.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.131435 restraints weight = 87899.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131819 restraints weight = 58214.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.132357 restraints weight = 43574.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.132457 restraints weight = 37522.307| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 36208 Z= 0.191 Angle : 0.659 11.065 49313 Z= 0.339 Chirality : 0.045 0.228 5556 Planarity : 0.005 0.119 6348 Dihedral : 4.950 45.801 4854 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.99 % Allowed : 14.43 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.44 % Cis-general : 0.23 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.12), residues: 4476 helix: 1.52 (0.20), residues: 691 sheet: -0.02 (0.14), residues: 1232 loop : -1.11 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1014 TYR 0.033 0.002 TYR C 904 PHE 0.035 0.002 PHE B 329 TRP 0.063 0.003 TRP A 886 HIS 0.012 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00451 (36159) covalent geometry : angle 0.65571 (49215) SS BOND : bond 0.00382 ( 49) SS BOND : angle 1.55816 ( 98) hydrogen bonds : bond 0.04057 ( 1174) hydrogen bonds : angle 5.23841 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6668.70 seconds wall clock time: 115 minutes 37.52 seconds (6937.52 seconds total)