Starting phenix.real_space_refine on Fri Mar 6 21:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a97_11687/03_2026/7a97_11687.map" } resolution = 4.4 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= 0.002 sd= 0.030 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 172 5.16 5 C 22119 2.51 5 N 5769 2.21 5 O 6566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.04s 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: 34626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8337 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 53, 'TRANS': 1011} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "C" Number of atoms: 8343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8343 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 5 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "E" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Time building chain proxies: 7.94, per 1000 atoms: 0.23 Number of scatterers: 34626 At special positions: 0 Unit cell: (184.338, 160.622, 250.096, 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 172 16.00 O 6566 8.00 N 5769 7.00 C 22119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8210 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 53 sheets defined 31.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.599A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 342 removed outlier: 4.399A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.593A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.599A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.856A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 3.716A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 782 removed outlier: 3.651A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 822 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.550A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.897A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.802A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.509A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.572A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.531A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 6.175A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.571A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.148A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.568A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 754' Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.791A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.586A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 removed outlier: 3.574A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 852 through 856' Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.685A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 4.095A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.870A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.582A pdb=" N ILE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 966 removed outlier: 4.296A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.560A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.027A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.570A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.923A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.707A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 747 through 754' Processing helix chain 'C' and resid 756 through 778 removed outlier: 3.714A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.959A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.692A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 852 through 856' Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.571A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 877 " --> pdb=" O TYR C 873 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 4.079A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.747A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.860A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 968 removed outlier: 4.038A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.582A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1032 removed outlier: 3.998A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.755A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.565A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.805A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 99 removed outlier: 3.631A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.953A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.921A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 176 removed outlier: 3.880A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.657A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 184 " --> pdb=" O TYR D 180 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 250 removed outlier: 3.855A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.614A pdb=" N LEU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.888A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.676A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 300' Processing helix chain 'D' and resid 304 through 318 removed outlier: 3.696A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.547A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 3.697A pdb=" N LEU D 370 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.631A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.610A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 414 through 421' Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.626A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 4.073A pdb=" N LYS D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D 463 " --> pdb=" O TRP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.515A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.752A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.593A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 529 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.918A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.888A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.524A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 588' Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.545A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.954A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 79 removed outlier: 4.034A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 99 removed outlier: 3.631A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.140A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.799A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 4.049A pdb=" N ALA E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.675A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.897A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 184 " --> pdb=" O TYR E 180 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 removed outlier: 4.054A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 248 removed outlier: 3.975A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.539A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 removed outlier: 3.635A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 removed outlier: 3.801A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 300' Processing helix chain 'E' and resid 305 through 314 removed outlier: 3.717A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.680A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 Processing helix chain 'E' and resid 371 through 383 removed outlier: 3.998A pdb=" N GLU E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.570A pdb=" N VAL E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 444 removed outlier: 3.947A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.686A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE E 464 " --> pdb=" O ARG E 460 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 482 removed outlier: 3.523A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 503 removed outlier: 3.687A pdb=" N LEU E 503 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 533 removed outlier: 3.878A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 561 removed outlier: 3.527A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.549A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.795A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 Processing helix chain 'E' and resid 598 through 602 removed outlier: 3.905A pdb=" N ASN E 601 " --> pdb=" O GLN E 598 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 602 " --> pdb=" O ASN E 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 598 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.068A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.894A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.759A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 145 removed outlier: 10.564A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.636A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.668A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.048A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.890A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.082A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 727 removed outlier: 6.766A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A1062 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.649A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.868A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 28 removed outlier: 4.080A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.786A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.508A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.132A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 278 through 279 removed outlier: 6.861A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 4.317A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.519A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.622A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.823A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.634A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.165A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 removed outlier: 3.552A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.878A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B1062 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 727 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 4.021A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 28 removed outlier: 4.033A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.777A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.526A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.671A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 160 removed outlier: 6.547A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 200 through 201 removed outlier: 3.968A pdb=" N PHE C 201 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.552A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.611A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 540 through 543 removed outlier: 3.524A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 551 through 554 removed outlier: 4.251A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 655 through 660 removed outlier: 5.404A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.722A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.830A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.871A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.610A pdb=" N THR E 347 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 359 " --> pdb=" O THR E 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 927 hydrogen bonds defined for protein. 2550 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: 8.09 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9513 1.33 - 1.45: 6584 1.45 - 1.57: 19135 1.57 - 1.69: 0 1.69 - 1.81: 244 Bond restraints: 35476 Sorted by residual: bond pdb=" N VAL A 729 " pdb=" CA VAL A 729 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.08e-02 8.57e+03 1.33e+01 bond pdb=" N ILE A 742 " pdb=" CA ILE A 742 " ideal model delta sigma weight residual 1.460 1.498 -0.037 1.19e-02 7.06e+03 9.89e+00 bond pdb=" N LEU E 424 " pdb=" CA LEU E 424 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.34e+00 bond pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.74e+00 bond pdb=" N VAL E 283 " pdb=" CA VAL E 283 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.71e+00 ... (remaining 35471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 47524 1.83 - 3.66: 638 3.66 - 5.49: 74 5.49 - 7.32: 5 7.32 - 9.15: 3 Bond angle restraints: 48244 Sorted by residual: angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.47 108.54 4.93 1.01e+00 9.80e-01 2.39e+01 angle pdb=" C CYS A 743 " pdb=" CA CYS A 743 " pdb=" CB CYS A 743 " ideal model delta sigma weight residual 110.51 119.66 -9.15 1.89e+00 2.80e-01 2.34e+01 angle pdb=" C CYS B 480 " pdb=" CA CYS B 480 " pdb=" CB CYS B 480 " ideal model delta sigma weight residual 117.07 110.27 6.80 1.44e+00 4.82e-01 2.23e+01 angle pdb=" N VAL E 318 " pdb=" CA VAL E 318 " pdb=" C VAL E 318 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA LEU E 423 " pdb=" C LEU E 423 " pdb=" O LEU E 423 " ideal model delta sigma weight residual 121.87 116.83 5.04 1.16e+00 7.43e-01 1.88e+01 ... (remaining 48239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 20547 13.18 - 26.37: 443 26.37 - 39.55: 103 39.55 - 52.74: 3 52.74 - 65.92: 4 Dihedral angle restraints: 21100 sinusoidal: 8342 harmonic: 12758 Sorted by residual: dihedral pdb=" C CYS A 743 " pdb=" N CYS A 743 " pdb=" CA CYS A 743 " pdb=" CB CYS A 743 " ideal model delta harmonic sigma weight residual -122.60 -141.06 18.46 0 2.50e+00 1.60e-01 5.45e+01 dihedral pdb=" N CYS A 743 " pdb=" C CYS A 743 " pdb=" CA CYS A 743 " pdb=" CB CYS A 743 " ideal model delta harmonic sigma weight residual 122.80 138.37 -15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -10.67 -62.33 1 2.00e+01 2.50e-03 1.29e+01 ... (remaining 21097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 5309 0.136 - 0.272: 27 0.272 - 0.408: 1 0.408 - 0.544: 0 0.544 - 0.680: 1 Chirality restraints: 5338 Sorted by residual: chirality pdb=" CA CYS A 743 " pdb=" N CYS A 743 " pdb=" C CYS A 743 " pdb=" CB CYS A 743 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA ASP A 745 " pdb=" N ASP A 745 " pdb=" C ASP A 745 " pdb=" CB ASP A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA GLU C 484 " pdb=" N GLU C 484 " pdb=" C GLU C 484 " pdb=" CB GLU C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5335 not shown) Planarity restraints: 6255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 328 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C ARG B 328 " -0.072 2.00e-02 2.50e+03 pdb=" O ARG B 328 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE B 329 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 316 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C VAL D 316 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL D 316 " -0.020 2.00e-02 2.50e+03 pdb=" N SER D 317 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 738 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C CYS A 738 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS A 738 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 739 " 0.016 2.00e-02 2.50e+03 ... (remaining 6252 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 261 2.64 - 3.20: 28782 3.20 - 3.77: 48584 3.77 - 4.33: 69475 4.33 - 4.90: 114261 Nonbonded interactions: 261363 Sorted by model distance: nonbonded pdb=" OG1 THR A 22 " pdb=" O THR A 76 " model vdw 2.074 3.040 nonbonded pdb=" O PHE B 541 " pdb=" OD1 ASN B 542 " model vdw 2.167 3.040 nonbonded pdb=" CD LYS A 97 " pdb=" O ASN A 185 " model vdw 2.181 3.440 nonbonded pdb=" OH TYR E 217 " pdb=" OD2 ASP E 225 " model vdw 2.221 3.040 nonbonded pdb=" CA LYS D 419 " pdb=" CD2 LEU D 424 " model vdw 2.228 3.890 ... (remaining 261358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 826 or resid 852 through 1146)) selection = (chain 'C' and (resid 14 through 617 or resid 641 through 1146)) } ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.00 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: 10.140 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.030 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.046 35524 Z= 0.173 Angle : 0.477 9.147 48340 Z= 0.303 Chirality : 0.042 0.680 5338 Planarity : 0.003 0.042 6255 Dihedral : 5.509 65.924 12746 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.28 % Favored : 89.70 % Rotamer: Outliers : 0.26 % Allowed : 3.31 % Favored : 96.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.10), residues: 4329 helix: -4.12 (0.07), residues: 1037 sheet: -1.81 (0.20), residues: 575 loop : -2.84 (0.09), residues: 2717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 457 TYR 0.005 0.000 TYR D 385 PHE 0.007 0.000 PHE A 543 TRP 0.003 0.000 TRP E 302 HIS 0.001 0.000 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00243 (35476) covalent geometry : angle 0.47730 (48244) SS BOND : bond 0.00181 ( 48) SS BOND : angle 0.30370 ( 96) hydrogen bonds : bond 0.34289 ( 927) hydrogen bonds : angle 9.55140 ( 2550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 369 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8652 (t) cc_final: 0.8230 (t) REVERT: A 513 LEU cc_start: 0.9575 (mt) cc_final: 0.9281 (tp) REVERT: A 780 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8055 (mm-30) REVERT: A 969 ASN cc_start: 0.8975 (m-40) cc_final: 0.8391 (m-40) REVERT: A 984 LEU cc_start: 0.9326 (mt) cc_final: 0.8800 (tp) REVERT: B 153 MET cc_start: 0.7673 (ptt) cc_final: 0.7417 (ptm) REVERT: B 307 THR cc_start: 0.8961 (m) cc_final: 0.8722 (p) REVERT: B 365 TYR cc_start: 0.8463 (m-80) cc_final: 0.8103 (m-10) REVERT: B 429 PHE cc_start: 0.7693 (t80) cc_final: 0.7377 (t80) REVERT: B 759 PHE cc_start: 0.8413 (m-10) cc_final: 0.8065 (m-80) REVERT: B 1033 VAL cc_start: 0.9343 (t) cc_final: 0.9018 (t) REVERT: C 88 ASP cc_start: 0.8975 (m-30) cc_final: 0.8765 (p0) REVERT: C 117 LEU cc_start: 0.8838 (tp) cc_final: 0.8580 (mt) REVERT: C 392 PHE cc_start: 0.7523 (m-80) cc_final: 0.7304 (m-80) REVERT: C 785 VAL cc_start: 0.9045 (m) cc_final: 0.8844 (p) REVERT: C 819 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8364 (mm-30) REVERT: C 1040 VAL cc_start: 0.9161 (t) cc_final: 0.8899 (t) REVERT: D 297 MET cc_start: 0.8622 (mtm) cc_final: 0.8356 (ptt) REVERT: D 494 ASP cc_start: 0.9023 (m-30) cc_final: 0.8800 (p0) REVERT: D 609 ASP cc_start: 0.9198 (t70) cc_final: 0.8926 (p0) REVERT: E 455 MET cc_start: 0.9741 (tmm) cc_final: 0.8935 (tmm) outliers start: 10 outliers final: 0 residues processed: 378 average time/residue: 0.2116 time to fit residues: 131.9199 Evaluate side-chains 174 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 10.0000 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 52 GLN A 81 ASN A 134 GLN A 218 GLN A 409 GLN A 414 GLN A 474 GLN A 493 GLN A 542 ASN A 564 GLN A 703 ASN A 751 ASN A 755 GLN A 762 GLN A 779 GLN A 787 GLN A 872 GLN A 920 GLN A 926 GLN A 935 GLN A 955 ASN A 992 GLN A1005 GLN A1010 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1106 GLN A1113 GLN B 14 GLN B 49 HIS B 61 ASN B 99 ASN B 115 GLN B 207 HIS B 218 GLN B 239 GLN B 271 GLN B 414 GLN B 437 ASN B 506 GLN B 613 GLN B 690 GLN B 755 GLN B 784 GLN B 787 GLN B 804 GLN B 901 GLN B 926 GLN B 954 GLN B 955 ASN B1048 HIS B1064 HIS B1071 GLN B1083 HIS C 23 GLN C 49 HIS C 69 HIS C 99 ASN C 115 GLN C 149 ASN C 173 GLN C 414 GLN C 498 GLN C 675 GLN C 690 GLN C 755 GLN C 762 GLN C 913 GLN C 914 ASN C 926 GLN C1010 GLN C1011 GLN C1036 GLN C1113 GLN C1134 ASN D 76 GLN D 86 GLN D 101 GLN D 287 GLN D 300 GLN D 380 GLN D 388 GLN D 508 ASN D 598 GLN E 60 GLN E 89 GLN E 96 GLN E 305 GLN E 340 GLN E 388 GLN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.062322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.045854 restraints weight = 358436.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.047165 restraints weight = 179979.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.047361 restraints weight = 110109.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.047945 restraints weight = 74733.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.047884 restraints weight = 62460.063| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35524 Z= 0.127 Angle : 0.518 7.699 48340 Z= 0.271 Chirality : 0.042 0.231 5338 Planarity : 0.004 0.044 6255 Dihedral : 2.647 22.254 4692 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.11), residues: 4329 helix: -1.33 (0.14), residues: 1107 sheet: -1.10 (0.21), residues: 569 loop : -2.43 (0.10), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 582 TYR 0.021 0.001 TYR D 199 PHE 0.037 0.001 PHE C1062 TRP 0.009 0.001 TRP D 203 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (35476) covalent geometry : angle 0.51695 (48244) SS BOND : bond 0.00244 ( 48) SS BOND : angle 0.87332 ( 96) hydrogen bonds : bond 0.07220 ( 927) hydrogen bonds : angle 5.92824 ( 2550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.295 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: A 177 MET cc_start: 0.0410 (ptt) cc_final: -0.0094 (ptt) REVERT: A 223 LEU cc_start: 0.8556 (tp) cc_final: 0.8202 (tp) REVERT: A 586 ASP cc_start: 0.8871 (t0) cc_final: 0.8433 (t0) REVERT: A 740 MET cc_start: 0.8077 (ttm) cc_final: 0.7267 (ttt) REVERT: A 780 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8769 (mt-10) REVERT: A 881 THR cc_start: 0.9404 (m) cc_final: 0.9135 (p) REVERT: A 984 LEU cc_start: 0.9392 (mt) cc_final: 0.8965 (tp) REVERT: B 153 MET cc_start: 0.8071 (ptt) cc_final: 0.7855 (ptm) REVERT: B 223 LEU cc_start: 0.9108 (tp) cc_final: 0.8757 (tp) REVERT: B 365 TYR cc_start: 0.8438 (m-80) cc_final: 0.8149 (m-10) REVERT: B 697 MET cc_start: 0.7838 (ptm) cc_final: 0.7638 (ttp) REVERT: B 936 ASP cc_start: 0.9051 (m-30) cc_final: 0.8754 (p0) REVERT: C 88 ASP cc_start: 0.8887 (m-30) cc_final: 0.8652 (p0) REVERT: C 191 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9036 (mp0) REVERT: C 731 MET cc_start: 0.9230 (ppp) cc_final: 0.7811 (ppp) REVERT: C 1050 MET cc_start: 0.8825 (pmm) cc_final: 0.8159 (pmm) REVERT: D 338 ASN cc_start: 0.9298 (t0) cc_final: 0.8856 (p0) REVERT: D 366 MET cc_start: 0.8646 (tpt) cc_final: 0.8199 (tpt) REVERT: D 494 ASP cc_start: 0.8972 (m-30) cc_final: 0.8738 (p0) REVERT: D 609 ASP cc_start: 0.9009 (t70) cc_final: 0.8768 (p0) REVERT: E 62 MET cc_start: 0.8842 (mpp) cc_final: 0.8526 (mpp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1976 time to fit residues: 65.7617 Evaluate side-chains 134 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 236 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 402 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 238 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 207 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 30 ASN B 66 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 481 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1134 ASN C 17 ASN C 66 HIS C 360 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C 953 ASN C1048 HIS D 34 HIS D 228 HIS E 98 GLN E 117 ASN E 239 HIS ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.058738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040394 restraints weight = 362239.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041524 restraints weight = 173244.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042206 restraints weight = 104176.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.042662 restraints weight = 73326.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.042888 restraints weight = 58003.081| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35524 Z= 0.173 Angle : 0.556 9.364 48340 Z= 0.286 Chirality : 0.041 0.182 5338 Planarity : 0.004 0.039 6255 Dihedral : 3.000 18.977 4692 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.03 % Allowed : 1.62 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4329 helix: -0.13 (0.15), residues: 1165 sheet: -0.71 (0.21), residues: 575 loop : -2.08 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 815 TYR 0.019 0.001 TYR B 248 PHE 0.040 0.001 PHE C1062 TRP 0.037 0.001 TRP E 478 HIS 0.012 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00360 (35476) covalent geometry : angle 0.55495 (48244) SS BOND : bond 0.00267 ( 48) SS BOND : angle 0.82733 ( 96) hydrogen bonds : bond 0.04847 ( 927) hydrogen bonds : angle 5.06394 ( 2550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.355 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 177 MET cc_start: 0.0038 (ptt) cc_final: -0.0701 (ptt) REVERT: A 223 LEU cc_start: 0.8564 (tp) cc_final: 0.8215 (tp) REVERT: A 513 LEU cc_start: 0.9631 (mm) cc_final: 0.9252 (tp) REVERT: A 740 MET cc_start: 0.8666 (ttm) cc_final: 0.8285 (ttm) REVERT: A 780 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8813 (mt-10) REVERT: A 869 MET cc_start: 0.9303 (ptp) cc_final: 0.9084 (ptp) REVERT: A 881 THR cc_start: 0.9471 (m) cc_final: 0.9139 (p) REVERT: B 223 LEU cc_start: 0.9093 (tp) cc_final: 0.8860 (tp) REVERT: B 365 TYR cc_start: 0.8895 (m-80) cc_final: 0.8464 (m-80) REVERT: B 740 MET cc_start: 0.8598 (ttt) cc_final: 0.8249 (ttt) REVERT: B 936 ASP cc_start: 0.9182 (m-30) cc_final: 0.8963 (p0) REVERT: B 1029 MET cc_start: 0.9526 (tpt) cc_final: 0.9289 (tpp) REVERT: C 88 ASP cc_start: 0.9007 (m-30) cc_final: 0.8655 (p0) REVERT: C 177 MET cc_start: 0.6669 (mtp) cc_final: 0.6424 (mtp) REVERT: C 731 MET cc_start: 0.9283 (ppp) cc_final: 0.8344 (ppp) REVERT: C 1040 VAL cc_start: 0.9550 (t) cc_final: 0.9348 (p) REVERT: C 1050 MET cc_start: 0.8856 (pmm) cc_final: 0.8191 (pmm) REVERT: D 360 MET cc_start: 0.7922 (mmp) cc_final: 0.7440 (mmm) REVERT: D 609 ASP cc_start: 0.9258 (t70) cc_final: 0.9000 (p0) REVERT: E 62 MET cc_start: 0.8956 (mpp) cc_final: 0.8606 (mpp) REVERT: E 82 MET cc_start: 0.9711 (ppp) cc_final: 0.9184 (pmm) REVERT: E 366 MET cc_start: 0.9029 (mmm) cc_final: 0.8688 (mmm) REVERT: E 579 MET cc_start: 0.5975 (mtp) cc_final: 0.5258 (mmt) outliers start: 1 outliers final: 1 residues processed: 148 average time/residue: 0.1945 time to fit residues: 50.5713 Evaluate side-chains 117 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 310 optimal weight: 1.9990 chunk 358 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 404 optimal weight: 8.9990 chunk 372 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN A 953 ASN B 211 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C1048 HIS D 34 HIS E 58 ASN ** E 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.057307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.038934 restraints weight = 361573.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040272 restraints weight = 181226.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.040566 restraints weight = 105617.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.041053 restraints weight = 71366.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041012 restraints weight = 67317.679| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35524 Z= 0.164 Angle : 0.511 7.955 48340 Z= 0.263 Chirality : 0.041 0.180 5338 Planarity : 0.003 0.038 6255 Dihedral : 3.154 21.326 4692 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4329 helix: 0.42 (0.15), residues: 1201 sheet: -0.66 (0.20), residues: 610 loop : -1.79 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.016 0.001 TYR B 904 PHE 0.016 0.001 PHE E 400 TRP 0.033 0.001 TRP A 886 HIS 0.014 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00333 (35476) covalent geometry : angle 0.51067 (48244) SS BOND : bond 0.00429 ( 48) SS BOND : angle 0.78650 ( 96) hydrogen bonds : bond 0.04147 ( 927) hydrogen bonds : angle 4.70622 ( 2550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1001 (ptt) cc_final: 0.0703 (ptt) REVERT: A 223 LEU cc_start: 0.8888 (tp) cc_final: 0.8557 (tp) REVERT: A 740 MET cc_start: 0.8776 (ttm) cc_final: 0.8221 (ttt) REVERT: A 780 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8829 (mt-10) REVERT: A 881 THR cc_start: 0.9589 (m) cc_final: 0.9278 (p) REVERT: B 223 LEU cc_start: 0.9143 (tp) cc_final: 0.8923 (tp) REVERT: B 365 TYR cc_start: 0.9184 (m-80) cc_final: 0.8734 (m-80) REVERT: B 731 MET cc_start: 0.9041 (ptp) cc_final: 0.8839 (ptp) REVERT: B 740 MET cc_start: 0.8700 (ttt) cc_final: 0.8384 (ttt) REVERT: B 1029 MET cc_start: 0.9483 (tpt) cc_final: 0.9258 (tpp) REVERT: C 88 ASP cc_start: 0.8947 (m-30) cc_final: 0.8599 (p0) REVERT: C 117 LEU cc_start: 0.9290 (tp) cc_final: 0.8921 (mt) REVERT: C 177 MET cc_start: 0.6880 (mtp) cc_final: 0.6481 (mtp) REVERT: C 223 LEU cc_start: 0.9214 (mm) cc_final: 0.9008 (mm) REVERT: C 697 MET cc_start: 0.8591 (tpp) cc_final: 0.8366 (tpp) REVERT: C 731 MET cc_start: 0.9007 (ppp) cc_final: 0.8529 (ppp) REVERT: C 1050 MET cc_start: 0.8579 (pmm) cc_final: 0.8059 (pmm) REVERT: D 338 ASN cc_start: 0.9126 (t0) cc_final: 0.8677 (p0) REVERT: D 360 MET cc_start: 0.8152 (mmp) cc_final: 0.7760 (mmm) REVERT: D 366 MET cc_start: 0.9019 (tpt) cc_final: 0.8647 (tpt) REVERT: D 609 ASP cc_start: 0.9052 (t70) cc_final: 0.8773 (p0) REVERT: E 62 MET cc_start: 0.9066 (mpp) cc_final: 0.8843 (mpp) REVERT: E 270 MET cc_start: 0.5660 (tpt) cc_final: 0.4384 (tpt) REVERT: E 366 MET cc_start: 0.8924 (mmm) cc_final: 0.8572 (mmm) REVERT: E 579 MET cc_start: 0.5758 (mtp) cc_final: 0.4767 (mmt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1992 time to fit residues: 46.2145 Evaluate side-chains 109 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 76 optimal weight: 0.2980 chunk 300 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 398 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 361 optimal weight: 0.9980 chunk 332 optimal weight: 20.0000 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 437 ASN B 506 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS D 524 GLN E 442 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.057791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.039201 restraints weight = 359535.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040299 restraints weight = 170293.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.041006 restraints weight = 102986.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.041429 restraints weight = 72525.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.041634 restraints weight = 58040.233| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 35524 Z= 0.095 Angle : 0.435 6.549 48340 Z= 0.220 Chirality : 0.040 0.207 5338 Planarity : 0.003 0.039 6255 Dihedral : 2.923 17.378 4692 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4329 helix: 0.92 (0.16), residues: 1183 sheet: -0.66 (0.21), residues: 600 loop : -1.64 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 204 TYR 0.008 0.001 TYR D 199 PHE 0.010 0.001 PHE C 855 TRP 0.020 0.001 TRP A 886 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00198 (35476) covalent geometry : angle 0.43478 (48244) SS BOND : bond 0.00159 ( 48) SS BOND : angle 0.52528 ( 96) hydrogen bonds : bond 0.03671 ( 927) hydrogen bonds : angle 4.40691 ( 2550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.396 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 177 MET cc_start: 0.0222 (ptt) cc_final: -0.0420 (ptt) REVERT: A 223 LEU cc_start: 0.8897 (tp) cc_final: 0.8572 (tp) REVERT: A 697 MET cc_start: 0.8080 (ptm) cc_final: 0.7746 (ptm) REVERT: A 740 MET cc_start: 0.8718 (ttm) cc_final: 0.8263 (ttm) REVERT: A 780 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8809 (mt-10) REVERT: A 881 THR cc_start: 0.9582 (m) cc_final: 0.9241 (p) REVERT: B 223 LEU cc_start: 0.9099 (tp) cc_final: 0.8875 (tp) REVERT: B 365 TYR cc_start: 0.9146 (m-80) cc_final: 0.8713 (m-80) REVERT: B 731 MET cc_start: 0.8981 (ptp) cc_final: 0.8778 (ptp) REVERT: B 740 MET cc_start: 0.8692 (ttt) cc_final: 0.8361 (ttt) REVERT: C 88 ASP cc_start: 0.8910 (m-30) cc_final: 0.8473 (p0) REVERT: C 153 MET cc_start: 0.8703 (pmm) cc_final: 0.8450 (pmm) REVERT: C 177 MET cc_start: 0.6775 (mtp) cc_final: 0.6442 (mtp) REVERT: C 223 LEU cc_start: 0.9261 (mm) cc_final: 0.9000 (mm) REVERT: C 392 PHE cc_start: 0.7812 (m-80) cc_final: 0.7567 (m-80) REVERT: C 731 MET cc_start: 0.9051 (ppp) cc_final: 0.8367 (ppp) REVERT: C 1030 SER cc_start: 0.9199 (m) cc_final: 0.8963 (t) REVERT: C 1050 MET cc_start: 0.8565 (pmm) cc_final: 0.8020 (pmm) REVERT: D 152 MET cc_start: -0.1727 (mtt) cc_final: -0.1967 (mtt) REVERT: D 338 ASN cc_start: 0.9016 (t0) cc_final: 0.8519 (p0) REVERT: D 360 MET cc_start: 0.8290 (mmp) cc_final: 0.7751 (mmm) REVERT: D 366 MET cc_start: 0.9177 (tpt) cc_final: 0.8795 (tpt) REVERT: D 609 ASP cc_start: 0.9302 (t70) cc_final: 0.9042 (p0) REVERT: E 62 MET cc_start: 0.8759 (mpp) cc_final: 0.8381 (mpp) REVERT: E 270 MET cc_start: 0.4575 (tpt) cc_final: 0.3593 (tpt) REVERT: E 366 MET cc_start: 0.9223 (mmm) cc_final: 0.8855 (mmm) REVERT: E 579 MET cc_start: 0.6558 (mtp) cc_final: 0.5897 (mmt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2052 time to fit residues: 47.1608 Evaluate side-chains 109 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 76 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 334 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 381 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 442 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.056975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.038324 restraints weight = 359788.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039283 restraints weight = 172467.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.039932 restraints weight = 104100.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.040384 restraints weight = 73910.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.040655 restraints weight = 59275.155| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35524 Z= 0.127 Angle : 0.457 7.802 48340 Z= 0.232 Chirality : 0.040 0.195 5338 Planarity : 0.003 0.038 6255 Dihedral : 2.995 17.936 4692 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4329 helix: 1.06 (0.16), residues: 1195 sheet: -0.66 (0.21), residues: 611 loop : -1.55 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1019 TYR 0.009 0.001 TYR B 396 PHE 0.019 0.001 PHE C1062 TRP 0.024 0.001 TRP A 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (35476) covalent geometry : angle 0.45664 (48244) SS BOND : bond 0.00172 ( 48) SS BOND : angle 0.54934 ( 96) hydrogen bonds : bond 0.03566 ( 927) hydrogen bonds : angle 4.36293 ( 2550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.135 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: A 177 MET cc_start: 0.0337 (ptt) cc_final: -0.0346 (ptt) REVERT: A 223 LEU cc_start: 0.8891 (tp) cc_final: 0.8551 (tp) REVERT: A 366 SER cc_start: 0.9450 (m) cc_final: 0.9230 (p) REVERT: A 697 MET cc_start: 0.8081 (ptm) cc_final: 0.7766 (ptm) REVERT: A 740 MET cc_start: 0.8744 (ttm) cc_final: 0.8189 (ttm) REVERT: A 780 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8818 (mt-10) REVERT: A 881 THR cc_start: 0.9598 (m) cc_final: 0.9311 (p) REVERT: B 223 LEU cc_start: 0.9078 (tp) cc_final: 0.8836 (tp) REVERT: B 365 TYR cc_start: 0.9223 (m-80) cc_final: 0.8833 (m-80) REVERT: B 740 MET cc_start: 0.8719 (ttt) cc_final: 0.8393 (ttt) REVERT: C 88 ASP cc_start: 0.8980 (m-30) cc_final: 0.8559 (p0) REVERT: C 117 LEU cc_start: 0.9241 (tp) cc_final: 0.8973 (mt) REVERT: C 153 MET cc_start: 0.8757 (pmm) cc_final: 0.8373 (pmm) REVERT: C 177 MET cc_start: 0.6731 (mtp) cc_final: 0.6411 (mtp) REVERT: C 223 LEU cc_start: 0.9283 (mm) cc_final: 0.8983 (mm) REVERT: C 392 PHE cc_start: 0.7850 (m-80) cc_final: 0.7594 (m-80) REVERT: C 731 MET cc_start: 0.9077 (ppp) cc_final: 0.8397 (ppp) REVERT: C 1030 SER cc_start: 0.9154 (m) cc_final: 0.8922 (t) REVERT: C 1050 MET cc_start: 0.8578 (pmm) cc_final: 0.8015 (pmm) REVERT: D 152 MET cc_start: -0.2438 (mtt) cc_final: -0.2925 (mtt) REVERT: D 338 ASN cc_start: 0.9022 (t0) cc_final: 0.8524 (p0) REVERT: D 360 MET cc_start: 0.8341 (mmp) cc_final: 0.7986 (mmm) REVERT: D 366 MET cc_start: 0.9165 (tpt) cc_final: 0.8757 (tpt) REVERT: D 609 ASP cc_start: 0.9258 (t70) cc_final: 0.8988 (p0) REVERT: E 270 MET cc_start: 0.4566 (tpt) cc_final: 0.3584 (tpt) REVERT: E 366 MET cc_start: 0.9241 (mmm) cc_final: 0.8862 (mmm) REVERT: E 579 MET cc_start: 0.6582 (mtp) cc_final: 0.5908 (tpp) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.2011 time to fit residues: 45.5887 Evaluate side-chains 109 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 286 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 388 optimal weight: 0.0050 chunk 48 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 320 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 493 GLN A 965 GLN B 271 GLN B 787 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.056781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.037936 restraints weight = 360924.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039038 restraints weight = 172279.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.039724 restraints weight = 103984.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040132 restraints weight = 74139.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040387 restraints weight = 59499.521| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35524 Z= 0.116 Angle : 0.455 8.272 48340 Z= 0.231 Chirality : 0.040 0.182 5338 Planarity : 0.003 0.039 6255 Dihedral : 3.031 16.775 4692 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4329 helix: 1.29 (0.16), residues: 1183 sheet: -0.59 (0.21), residues: 621 loop : -1.44 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 204 TYR 0.009 0.001 TYR B 396 PHE 0.026 0.001 PHE B 592 TRP 0.022 0.001 TRP A 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00242 (35476) covalent geometry : angle 0.45513 (48244) SS BOND : bond 0.00160 ( 48) SS BOND : angle 0.51621 ( 96) hydrogen bonds : bond 0.03387 ( 927) hydrogen bonds : angle 4.27298 ( 2550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.330 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 177 MET cc_start: 0.0392 (ptt) cc_final: -0.0285 (ptt) REVERT: A 223 LEU cc_start: 0.8937 (tp) cc_final: 0.8606 (tp) REVERT: A 697 MET cc_start: 0.8088 (ptm) cc_final: 0.7667 (ptm) REVERT: A 740 MET cc_start: 0.8750 (ttm) cc_final: 0.8147 (ttm) REVERT: A 780 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8812 (mt-10) REVERT: B 223 LEU cc_start: 0.9059 (tp) cc_final: 0.8806 (tp) REVERT: B 365 TYR cc_start: 0.9312 (m-80) cc_final: 0.8912 (m-80) REVERT: B 740 MET cc_start: 0.8825 (ttt) cc_final: 0.8610 (ttt) REVERT: B 773 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8780 (mt-10) REVERT: B 1029 MET cc_start: 0.9323 (tpp) cc_final: 0.9118 (tpp) REVERT: C 88 ASP cc_start: 0.8917 (m-30) cc_final: 0.8450 (p0) REVERT: C 117 LEU cc_start: 0.9231 (tp) cc_final: 0.8965 (mt) REVERT: C 177 MET cc_start: 0.6919 (mtp) cc_final: 0.6535 (mtp) REVERT: C 392 PHE cc_start: 0.7829 (m-80) cc_final: 0.7582 (m-80) REVERT: C 731 MET cc_start: 0.9059 (ppp) cc_final: 0.8396 (ppp) REVERT: C 1050 MET cc_start: 0.8579 (pmm) cc_final: 0.8011 (pmm) REVERT: D 152 MET cc_start: -0.2144 (mtt) cc_final: -0.2737 (mtt) REVERT: D 338 ASN cc_start: 0.8953 (t0) cc_final: 0.8446 (p0) REVERT: D 360 MET cc_start: 0.8423 (mmp) cc_final: 0.8061 (mmm) REVERT: D 366 MET cc_start: 0.9195 (tpt) cc_final: 0.8772 (tpt) REVERT: D 609 ASP cc_start: 0.9277 (t70) cc_final: 0.9003 (p0) REVERT: E 270 MET cc_start: 0.4406 (tpt) cc_final: 0.3523 (tpt) REVERT: E 579 MET cc_start: 0.6575 (mtp) cc_final: 0.5917 (tpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2009 time to fit residues: 44.2713 Evaluate side-chains 107 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 83 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 360 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 281 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 498 GLN A 607 GLN B 188 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 955 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN B1135 ASN C 69 HIS C 498 GLN C 519 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 241 HIS E 442 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.054414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035018 restraints weight = 362626.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.035979 restraints weight = 175415.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.036575 restraints weight = 107392.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036995 restraints weight = 77424.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.037174 restraints weight = 62498.866| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 35524 Z= 0.265 Angle : 0.648 11.313 48340 Z= 0.332 Chirality : 0.043 0.194 5338 Planarity : 0.004 0.054 6255 Dihedral : 3.880 19.067 4692 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4329 helix: 0.66 (0.15), residues: 1255 sheet: -0.63 (0.20), residues: 650 loop : -1.52 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 328 TYR 0.020 0.002 TYR B 396 PHE 0.029 0.002 PHE B 592 TRP 0.042 0.002 TRP A 886 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00533 (35476) covalent geometry : angle 0.64779 (48244) SS BOND : bond 0.00289 ( 48) SS BOND : angle 0.92972 ( 96) hydrogen bonds : bond 0.04220 ( 927) hydrogen bonds : angle 4.94548 ( 2550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0577 (ptt) cc_final: 0.0019 (ptt) REVERT: A 223 LEU cc_start: 0.9171 (tp) cc_final: 0.8856 (tp) REVERT: A 611 LEU cc_start: 0.9693 (tp) cc_final: 0.9476 (tt) REVERT: A 740 MET cc_start: 0.8786 (ttm) cc_final: 0.8288 (ttm) REVERT: A 780 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8757 (mt-10) REVERT: A 902 MET cc_start: 0.9193 (tpp) cc_final: 0.8762 (tpp) REVERT: A 1029 MET cc_start: 0.9330 (tpp) cc_final: 0.9093 (tpp) REVERT: B 223 LEU cc_start: 0.9141 (tp) cc_final: 0.8899 (tp) REVERT: B 365 TYR cc_start: 0.9500 (m-80) cc_final: 0.9148 (m-80) REVERT: B 773 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8782 (mt-10) REVERT: B 1029 MET cc_start: 0.9591 (tpp) cc_final: 0.9390 (tpp) REVERT: B 1050 MET cc_start: 0.9094 (pmm) cc_final: 0.8414 (pmm) REVERT: C 88 ASP cc_start: 0.9129 (m-30) cc_final: 0.8641 (p0) REVERT: C 153 MET cc_start: 0.9299 (pmm) cc_final: 0.8592 (pmm) REVERT: C 177 MET cc_start: 0.6630 (mtp) cc_final: 0.6240 (mtp) REVERT: C 392 PHE cc_start: 0.8010 (m-80) cc_final: 0.7777 (m-80) REVERT: C 731 MET cc_start: 0.8998 (ppp) cc_final: 0.8453 (ppp) REVERT: C 1050 MET cc_start: 0.8455 (pmm) cc_final: 0.7973 (pmm) REVERT: D 152 MET cc_start: -0.2419 (mtt) cc_final: -0.3099 (mtt) REVERT: D 338 ASN cc_start: 0.8950 (t0) cc_final: 0.8444 (p0) REVERT: D 360 MET cc_start: 0.8592 (mmp) cc_final: 0.8349 (mmm) REVERT: D 366 MET cc_start: 0.9290 (tpt) cc_final: 0.8834 (tpt) REVERT: D 609 ASP cc_start: 0.9174 (t70) cc_final: 0.8882 (p0) REVERT: E 62 MET cc_start: 0.8722 (mpp) cc_final: 0.8386 (mpp) REVERT: E 270 MET cc_start: 0.4747 (tpt) cc_final: 0.3856 (tpt) REVERT: E 366 MET cc_start: 0.9152 (tpt) cc_final: 0.8733 (mmm) REVERT: E 579 MET cc_start: 0.6870 (mtp) cc_final: 0.6386 (tpp) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1987 time to fit residues: 38.6525 Evaluate side-chains 94 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 137 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 208 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN B 271 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.055557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036666 restraints weight = 358471.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.037647 restraints weight = 168916.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038246 restraints weight = 102235.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.038681 restraints weight = 73365.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038919 restraints weight = 59223.575| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35524 Z= 0.122 Angle : 0.490 10.798 48340 Z= 0.250 Chirality : 0.041 0.168 5338 Planarity : 0.003 0.040 6255 Dihedral : 3.569 32.142 4692 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.77 (0.13), residues: 4329 helix: 1.08 (0.15), residues: 1241 sheet: -0.55 (0.21), residues: 644 loop : -1.40 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 204 TYR 0.010 0.001 TYR B 396 PHE 0.011 0.001 PHE C 855 TRP 0.032 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00257 (35476) covalent geometry : angle 0.48737 (48244) SS BOND : bond 0.00262 ( 48) SS BOND : angle 1.30879 ( 96) hydrogen bonds : bond 0.03664 ( 927) hydrogen bonds : angle 4.46244 ( 2550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0484 (ptt) cc_final: -0.0020 (ptt) REVERT: A 223 LEU cc_start: 0.9155 (tp) cc_final: 0.8832 (tp) REVERT: A 740 MET cc_start: 0.8796 (ttm) cc_final: 0.8207 (ttm) REVERT: A 902 MET cc_start: 0.9120 (tpp) cc_final: 0.8676 (tpp) REVERT: B 223 LEU cc_start: 0.9124 (tp) cc_final: 0.8883 (tp) REVERT: B 365 TYR cc_start: 0.9436 (m-80) cc_final: 0.9054 (m-80) REVERT: B 773 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8757 (mt-10) REVERT: B 779 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9048 (mp10) REVERT: B 1029 MET cc_start: 0.9554 (tpp) cc_final: 0.9223 (tpp) REVERT: B 1050 MET cc_start: 0.9104 (pmm) cc_final: 0.8465 (pmm) REVERT: C 88 ASP cc_start: 0.9086 (m-30) cc_final: 0.8539 (p0) REVERT: C 153 MET cc_start: 0.9264 (pmm) cc_final: 0.8509 (pmm) REVERT: C 177 MET cc_start: 0.6668 (mtp) cc_final: 0.6352 (mtp) REVERT: C 392 PHE cc_start: 0.7976 (m-80) cc_final: 0.7729 (m-80) REVERT: C 731 MET cc_start: 0.9050 (ppp) cc_final: 0.8461 (ppp) REVERT: C 1050 MET cc_start: 0.8483 (pmm) cc_final: 0.7881 (pmm) REVERT: D 152 MET cc_start: -0.2336 (mtt) cc_final: -0.3037 (mtt) REVERT: D 338 ASN cc_start: 0.9001 (t0) cc_final: 0.8499 (p0) REVERT: D 360 MET cc_start: 0.8518 (mmp) cc_final: 0.8159 (mmm) REVERT: D 366 MET cc_start: 0.9262 (tpt) cc_final: 0.8762 (tpt) REVERT: D 609 ASP cc_start: 0.9160 (t70) cc_final: 0.8863 (p0) REVERT: E 62 MET cc_start: 0.8889 (mpp) cc_final: 0.8576 (mpp) REVERT: E 270 MET cc_start: 0.4549 (tpt) cc_final: 0.3735 (tpt) REVERT: E 366 MET cc_start: 0.9261 (tpt) cc_final: 0.9017 (mmm) REVERT: E 579 MET cc_start: 0.6729 (mtp) cc_final: 0.6230 (tpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1900 time to fit residues: 37.0356 Evaluate side-chains 103 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 287 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 401 optimal weight: 30.0000 chunk 249 optimal weight: 9.9990 chunk 431 optimal weight: 30.0000 chunk 209 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 230 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 580 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 493 HIS E 34 HIS E 51 ASN E 290 ASN E 442 GLN E 522 GLN ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.053736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034317 restraints weight = 362836.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.035261 restraints weight = 174308.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.035927 restraints weight = 106899.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036306 restraints weight = 77994.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.036519 restraints weight = 63708.838| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35524 Z= 0.259 Angle : 0.663 12.079 48340 Z= 0.340 Chirality : 0.043 0.209 5338 Planarity : 0.004 0.059 6255 Dihedral : 4.236 37.360 4692 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.08 (0.13), residues: 4329 helix: 0.67 (0.15), residues: 1287 sheet: -0.80 (0.20), residues: 660 loop : -1.51 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1107 TYR 0.021 0.002 TYR B 396 PHE 0.031 0.002 PHE C 58 TRP 0.077 0.002 TRP A 886 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00540 (35476) covalent geometry : angle 0.66162 (48244) SS BOND : bond 0.00315 ( 48) SS BOND : angle 1.22065 ( 96) hydrogen bonds : bond 0.04179 ( 927) hydrogen bonds : angle 4.99668 ( 2550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8658 Ramachandran restraints generated. 4329 Oldfield, 0 Emsley, 4329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0401 (ptt) cc_final: -0.0317 (ptt) REVERT: A 223 LEU cc_start: 0.9231 (tp) cc_final: 0.8907 (tp) REVERT: A 740 MET cc_start: 0.8804 (ttm) cc_final: 0.8220 (ttm) REVERT: A 780 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 223 LEU cc_start: 0.9181 (tp) cc_final: 0.8953 (tp) REVERT: B 365 TYR cc_start: 0.9507 (m-80) cc_final: 0.9134 (m-80) REVERT: B 740 MET cc_start: 0.8722 (ttt) cc_final: 0.8485 (ttt) REVERT: B 1050 MET cc_start: 0.9141 (pmm) cc_final: 0.8391 (pmm) REVERT: C 177 MET cc_start: 0.6949 (mtp) cc_final: 0.6586 (mtp) REVERT: C 392 PHE cc_start: 0.8121 (m-80) cc_final: 0.7841 (m-80) REVERT: C 731 MET cc_start: 0.8904 (ppp) cc_final: 0.8430 (ppp) REVERT: C 1050 MET cc_start: 0.8332 (pmm) cc_final: 0.7706 (pmm) REVERT: D 123 MET cc_start: 0.9430 (ptm) cc_final: 0.8991 (ptt) REVERT: D 152 MET cc_start: -0.1941 (mtt) cc_final: -0.2730 (mtp) REVERT: D 338 ASN cc_start: 0.9023 (t0) cc_final: 0.8510 (p0) REVERT: D 360 MET cc_start: 0.8607 (mmp) cc_final: 0.8262 (mmm) REVERT: D 366 MET cc_start: 0.9363 (tpt) cc_final: 0.8862 (tpt) REVERT: D 609 ASP cc_start: 0.9231 (t70) cc_final: 0.8947 (p0) REVERT: E 62 MET cc_start: 0.8928 (mpp) cc_final: 0.8607 (mpp) REVERT: E 270 MET cc_start: 0.4656 (tpt) cc_final: 0.4388 (tpt) REVERT: E 366 MET cc_start: 0.9320 (tpt) cc_final: 0.8890 (mmm) REVERT: E 579 MET cc_start: 0.7381 (mtp) cc_final: 0.6985 (tpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2000 time to fit residues: 37.7124 Evaluate side-chains 90 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 50 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 260 optimal weight: 0.0170 chunk 372 optimal weight: 0.0370 chunk 292 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 607 GLN B 271 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 442 GLN E 522 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.053558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034275 restraints weight = 330765.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034065 restraints weight = 173491.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034485 restraints weight = 124308.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.034572 restraints weight = 100650.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034606 restraints weight = 88290.421| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35524 Z= 0.092 Angle : 0.485 9.373 48340 Z= 0.245 Chirality : 0.042 0.193 5338 Planarity : 0.003 0.044 6255 Dihedral : 3.632 36.678 4692 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.63 (0.13), residues: 4329 helix: 1.23 (0.15), residues: 1270 sheet: -0.51 (0.20), residues: 658 loop : -1.34 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 204 TYR 0.010 0.001 TYR B 265 PHE 0.012 0.001 PHE C 58 TRP 0.028 0.001 TRP A 886 HIS 0.010 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00198 (35476) covalent geometry : angle 0.48298 (48244) SS BOND : bond 0.00241 ( 48) SS BOND : angle 1.10890 ( 96) hydrogen bonds : bond 0.03540 ( 927) hydrogen bonds : angle 4.34634 ( 2550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7243.41 seconds wall clock time: 125 minutes 31.27 seconds (7531.27 seconds total)