Starting phenix.real_space_refine on Mon Sep 14 10:49:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk9_32563/09_2026/7wk9_32563.map" } resolution = 3.48 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= 0.032 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 133 5.16 5 C 18997 2.51 5 N 4964 2.21 5 O 5651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29745 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8165 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 54, 'TRANS': 987} Chain breaks: 7 Chain: "C" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "c" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "d" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 841 Classifications: {'peptide': 111} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 8239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8239 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 54, 'TRANS': 996} Chain breaks: 7 Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1662 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1656 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 6.61, per 1000 atoms: 0.22 Number of scatterers: 29745 At special positions: 0 Unit cell: (185.81, 137.718, 196.74, 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 133 16.00 O 5651 8.00 N 4964 7.00 C 18997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 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 c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 202 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 92 " distance=2.03 Simple disulfide: pdb=" SG CYS b 138 " - pdb=" SG CYS b 198 " 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 67 sheets defined 18.3% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.736A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.856A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.622A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.827A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.026A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.503A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 909 removed outlier: 3.719A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.735A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.613A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 960 removed outlier: 3.710A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 removed outlier: 3.745A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.553A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 988 through 1031 removed outlier: 3.993A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.673A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.378A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.694A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.958A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.790A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.892A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 752' Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.913A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.511A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.879A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.601A pdb=" N ALA C 876 " --> pdb=" O GLN C 872 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 906 removed outlier: 3.913A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.814A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.609A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 928 " --> pdb=" O ALA C 924 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 963 removed outlier: 3.820A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.571A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.871A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.812A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 56 No H-bonds generated for 'chain 'd' and resid 54 through 56' Processing helix chain 'd' and resid 83 through 87 removed outlier: 4.106A pdb=" N ALA d 87 " --> pdb=" O GLU d 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.617A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.262A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.527A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.813A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.763A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.932A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 824 removed outlier: 3.860A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.814A pdb=" N ALA B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.601A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 928 " --> pdb=" O ALA B 924 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 963 removed outlier: 3.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.660A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.644A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.901A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 removed outlier: 3.581A pdb=" N ARG a 31 " --> pdb=" O SER a 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE a 32 " --> pdb=" O PHE a 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 28 through 32' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.879A pdb=" N SER a 91 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 198 removed outlier: 4.014A pdb=" N SER a 197 " --> pdb=" O SER a 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 4.245A pdb=" N ALA b 87 " --> pdb=" O GLU b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 132 removed outlier: 3.560A pdb=" N LEU b 129 " --> pdb=" O SER b 125 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER b 131 " --> pdb=" O GLU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 192 removed outlier: 3.892A pdb=" N ARG b 192 " --> pdb=" O ASP b 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.524A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.780A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.525A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.534A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.853A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.507A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.590A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.209A pdb=" N ASN A 450 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N ARG A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.075A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.691A 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 654 through 655 removed outlier: 5.765A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.456A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.634A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1060 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.613A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.923A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.506A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.745A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.633A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.005A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.684A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.566A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.514A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.952A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.720A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.721A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.663A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.972A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'c' and resid 9 through 11 removed outlier: 3.757A pdb=" N TYR c 95 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL c 37 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET c 34 " --> pdb=" O MET c 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG c 40 " --> pdb=" O GLY c 44 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU c 57 " --> pdb=" O HIS c 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 9 through 11 removed outlier: 6.667A pdb=" N CYS c 96 " --> pdb=" O TRP c 110 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TRP c 110 " --> pdb=" O CYS c 96 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG c 98 " --> pdb=" O ALA c 108 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP c 106 " --> pdb=" O ASP c 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 17 through 23 removed outlier: 3.827A pdb=" N MET c 81 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.812A pdb=" N SER d 7 " --> pdb=" O SER d 22 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS d 23 " --> pdb=" O PHE d 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE d 75 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP d 74 " --> pdb=" O SER d 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER d 71 " --> pdb=" O ASP d 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 10 through 14 removed outlier: 6.628A pdb=" N LEU d 11 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS d 111 " --> pdb=" O LEU d 11 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL d 13 " --> pdb=" O LYS d 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 52 through 53 Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.595A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.629A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.762A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 244 through 245 Processing sheet with id=AF1, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.393A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.882A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.879A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.678A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.749A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AF8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.681A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AG1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.841A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG3, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS a 99 " --> pdb=" O TRP a 33 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP a 33 " --> pdb=" O LYS a 99 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET a 34 " --> pdb=" O MET a 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG a 40 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 9 through 12 removed outlier: 3.709A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA a 92 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG a 98 " --> pdb=" O TYR a 109 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR a 109 " --> pdb=" O ARG a 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 17 through 23 removed outlier: 3.757A pdb=" N THR a 71 " --> pdb=" O TYR a 80 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER a 187 " --> pdb=" O HIS a 171 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 127 through 131 removed outlier: 6.402A pdb=" N TYR a 182 " --> pdb=" O GLY a 151 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.539A pdb=" N THR a 211 " --> pdb=" O HIS a 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 5 through 7 removed outlier: 3.701A pdb=" N SER b 7 " --> pdb=" O SER b 22 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS b 23 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 75 " --> pdb=" O CYS b 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP b 74 " --> pdb=" O SER b 71 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP b 39 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN b 41 " --> pdb=" O LYS b 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 10 through 13 removed outlier: 6.256A pdb=" N LEU b 11 " --> pdb=" O GLU b 109 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS b 94 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA b 101 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 118 through 122 removed outlier: 3.540A pdb=" N VAL b 137 " --> pdb=" O PHE b 122 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR b 177 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 157 through 158 removed outlier: 3.829A pdb=" N TYR b 196 " --> pdb=" O PHE b 213 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE b 213 " --> pdb=" O TYR b 196 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA b 200 " --> pdb=" O ILE b 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE b 209 " --> pdb=" O ALA b 200 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2418 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: 8.31 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9136 1.34 - 1.46: 6545 1.46 - 1.58: 14606 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 30457 Sorted by residual: bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.87e+01 bond pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.85e+01 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.334 1.433 -0.099 2.34e-02 1.83e+03 1.78e+01 bond pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.43e+01 bond pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.11e-02 8.12e+03 1.07e+01 ... (remaining 30452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 40420 2.19 - 4.39: 872 4.39 - 6.58: 105 6.58 - 8.78: 27 8.78 - 10.97: 9 Bond angle restraints: 41433 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLY B 639 " pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C GLY C 639 " pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sigma weight residual 117.23 110.67 6.56 1.36e+00 5.41e-01 2.33e+01 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.37 119.37 -6.00 1.34e+00 5.57e-01 2.00e+01 ... (remaining 41428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 17711 17.42 - 34.84: 341 34.84 - 52.27: 110 52.27 - 69.69: 15 69.69 - 87.11: 2 Dihedral angle restraints: 18179 sinusoidal: 7093 harmonic: 11086 Sorted by residual: dihedral pdb=" CA LYS B 795 " pdb=" C LYS B 795 " pdb=" N TYR B 796 " pdb=" CA TYR B 796 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR a 101 " pdb=" C TYR a 101 " pdb=" N ASP a 102 " pdb=" CA ASP a 102 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG C 634 " pdb=" C ARG C 634 " pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 18176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3570 0.056 - 0.112: 863 0.112 - 0.169: 199 0.169 - 0.225: 31 0.225 - 0.281: 8 Chirality restraints: 4671 Sorted by residual: chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE b 121 " pdb=" CA ILE b 121 " pdb=" CG1 ILE b 121 " pdb=" CG2 ILE b 121 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 4668 not shown) Planarity restraints: 5342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 295 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 445 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C VAL A 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 445 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 446 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B 987 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.040 5.00e-02 4.00e+02 ... (remaining 5339 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 9257 2.85 - 3.37: 22275 3.37 - 3.88: 47980 3.88 - 4.39: 50056 4.39 - 4.90: 90211 Nonbonded interactions: 219779 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.342 3.040 nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.345 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.351 3.040 nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.351 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.352 3.040 ... (remaining 219774 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 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.600 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.120 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 : 0.005 0.099 30500 Z= 0.255 Angle : 0.785 10.974 41519 Z= 0.459 Chirality : 0.053 0.281 4671 Planarity : 0.006 0.082 5342 Dihedral : 8.279 87.110 10914 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -2.70 (0.11), residues: 3749 helix: -4.92 (0.05), residues: 574 sheet: -0.20 (0.16), residues: 750 loop : -1.57 (0.10), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.032 0.002 TYR d 53 PHE 0.026 0.003 PHE B 490 TRP 0.021 0.002 TRP a 33 HIS 0.012 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.25 (30457) covalent geometry : angle 0.78517 / 0.46 (41433) SS BOND : bond 0.00196 / 0.12 ( 43) SS BOND : angle 0.86498 / 0.58 ( 86) hydrogen bonds : bond 0.32302 / 21.23 ( 853) hydrogen bonds : angle 11.13310 / 7.62 ( 2418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 930 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5319 (mtt-85) cc_final: 0.4502 (ttp80) REVERT: A 95 ILE cc_start: 0.7552 (mt) cc_final: 0.7286 (tp) REVERT: A 168 PHE cc_start: 0.7527 (t80) cc_final: 0.7158 (t80) REVERT: A 196 ASN cc_start: 0.7666 (t0) cc_final: 0.7360 (t0) REVERT: A 270 LEU cc_start: 0.7719 (mp) cc_final: 0.6487 (mp) REVERT: A 309 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 654 GLU cc_start: 0.7186 (tt0) cc_final: 0.6947 (tt0) REVERT: A 780 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 804 GLN cc_start: 0.7882 (mt0) cc_final: 0.7605 (mt0) REVERT: A 868 GLU cc_start: 0.8262 (tt0) cc_final: 0.8036 (tt0) REVERT: A 883 THR cc_start: 0.8317 (p) cc_final: 0.7402 (m) REVERT: A 969 LYS cc_start: 0.8296 (mttt) cc_final: 0.7549 (mmmt) REVERT: A 979 ASP cc_start: 0.7340 (m-30) cc_final: 0.7005 (t0) REVERT: A 984 LEU cc_start: 0.7935 (mt) cc_final: 0.7638 (mm) REVERT: A 985 ASP cc_start: 0.7778 (m-30) cc_final: 0.7415 (m-30) REVERT: C 33 THR cc_start: 0.7954 (p) cc_final: 0.7620 (p) REVERT: C 36 VAL cc_start: 0.8567 (t) cc_final: 0.8339 (p) REVERT: C 81 ASN cc_start: 0.8323 (t0) cc_final: 0.8060 (m-40) REVERT: C 201 PHE cc_start: 0.8229 (t80) cc_final: 0.7994 (t80) REVERT: C 287 ASP cc_start: 0.7801 (t0) cc_final: 0.7573 (t0) REVERT: C 293 LEU cc_start: 0.8451 (tp) cc_final: 0.8114 (tp) REVERT: C 300 LYS cc_start: 0.9079 (mttt) cc_final: 0.8723 (mtmm) REVERT: C 303 LEU cc_start: 0.8761 (mt) cc_final: 0.8469 (tp) REVERT: C 353 TRP cc_start: 0.5844 (p90) cc_final: 0.5535 (p90) REVERT: C 515 PHE cc_start: 0.7210 (m-10) cc_final: 0.6788 (m-80) REVERT: C 528 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6204 (mmtm) REVERT: C 537 LYS cc_start: 0.8522 (tptt) cc_final: 0.8144 (tptp) REVERT: C 721 SER cc_start: 0.8065 (t) cc_final: 0.7746 (p) REVERT: C 752 LEU cc_start: 0.9209 (mt) cc_final: 0.8959 (tt) REVERT: C 755 GLN cc_start: 0.7462 (mt0) cc_final: 0.6869 (mp10) REVERT: C 795 LYS cc_start: 0.7440 (mttt) cc_final: 0.7235 (mttt) REVERT: C 884 SER cc_start: 0.8285 (m) cc_final: 0.8066 (t) REVERT: C 898 PHE cc_start: 0.6427 (t80) cc_final: 0.6180 (t80) REVERT: C 935 GLN cc_start: 0.8421 (tt0) cc_final: 0.7998 (tt0) REVERT: C 969 LYS cc_start: 0.8574 (mttt) cc_final: 0.8200 (mtmm) REVERT: C 1055 SER cc_start: 0.6945 (m) cc_final: 0.6458 (t) REVERT: C 1111 GLU cc_start: 0.7591 (tt0) cc_final: 0.7290 (tt0) REVERT: C 1116 THR cc_start: 0.7960 (p) cc_final: 0.7148 (p) REVERT: C 1145 LEU cc_start: 0.7569 (mt) cc_final: 0.7255 (mt) REVERT: c 34 MET cc_start: 0.5311 (mmm) cc_final: 0.4470 (mmm) REVERT: B 33 THR cc_start: 0.7988 (p) cc_final: 0.7720 (t) REVERT: B 84 LEU cc_start: 0.7912 (mt) cc_final: 0.7463 (mp) REVERT: B 133 PHE cc_start: 0.5580 (m-10) cc_final: 0.5179 (m-10) REVERT: B 285 ILE cc_start: 0.8005 (mt) cc_final: 0.7400 (mm) REVERT: B 340 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7651 (mp0) REVERT: B 353 TRP cc_start: 0.6165 (p90) cc_final: 0.5812 (p90) REVERT: B 384 PRO cc_start: 0.8013 (Cg_endo) cc_final: 0.7629 (Cg_exo) REVERT: B 535 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7045 (tmtt) REVERT: B 537 LYS cc_start: 0.8066 (tptt) cc_final: 0.7688 (tptp) REVERT: B 581 THR cc_start: 0.6717 (p) cc_final: 0.5215 (m) REVERT: B 583 GLU cc_start: 0.5418 (mt-10) cc_final: 0.5059 (mt-10) REVERT: B 654 GLU cc_start: 0.7698 (tt0) cc_final: 0.7418 (tt0) REVERT: B 726 ILE cc_start: 0.8793 (mp) cc_final: 0.8520 (mt) REVERT: B 730 SER cc_start: 0.8893 (p) cc_final: 0.8673 (t) REVERT: B 745 ASP cc_start: 0.8045 (m-30) cc_final: 0.7769 (p0) REVERT: B 814 LYS cc_start: 0.8723 (mttt) cc_final: 0.8447 (mmmt) REVERT: B 884 SER cc_start: 0.7823 (m) cc_final: 0.7511 (t) REVERT: B 969 LYS cc_start: 0.8824 (mttt) cc_final: 0.8370 (mmtm) REVERT: B 979 ASP cc_start: 0.8572 (m-30) cc_final: 0.7929 (t0) REVERT: B 1000 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7463 (mmt90) REVERT: a 31 ARG cc_start: 0.6126 (mmt180) cc_final: 0.5894 (mmm160) REVERT: a 38 LYS cc_start: 0.7912 (tttt) cc_final: 0.7490 (tttt) REVERT: a 64 PHE cc_start: 0.8560 (m-10) cc_final: 0.8271 (m-10) REVERT: a 69 THR cc_start: 0.6317 (m) cc_final: 0.5628 (p) REVERT: a 73 ASP cc_start: 0.7739 (t0) cc_final: 0.7436 (t0) REVERT: a 76 SER cc_start: 0.8782 (m) cc_final: 0.8557 (p) REVERT: a 153 PHE cc_start: 0.8320 (t80) cc_final: 0.7716 (t80) REVERT: b 46 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7746 (mm-40) REVERT: b 145 PRO cc_start: 0.5588 (Cg_endo) cc_final: 0.5132 (Cg_exo) outliers start: 12 outliers final: 6 residues processed: 940 average time/residue: 0.2003 time to fit residues: 294.2424 Evaluate side-chains 682 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 675 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain a residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 394 ASN A 703 ASN A 755 GLN A 787 GLN A 895 GLN A 955 ASN A 960 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN C 99 ASN C 207 HIS C 239 GLN C 519 HIS C 532 ASN C 717 ASN C 762 GLN C 895 GLN C 901 GLN C1101 HIS c 52 HIS d 6 GLN B 66 HIS B 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 544 ASN B 717 ASN B 955 ASN B1054 GLN B1083 HIS B1088 HIS B1113 GLN b 93 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.185211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147339 restraints weight = 69656.431| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.28 r_work: 0.3803 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30500 Z= 0.252 Angle : 0.721 8.281 41519 Z= 0.381 Chirality : 0.048 0.248 4671 Planarity : 0.005 0.059 5342 Dihedral : 5.270 53.220 4101 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.13 % Allowed : 8.59 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -1.63 (0.12), residues: 3749 helix: -2.69 (0.15), residues: 616 sheet: 0.25 (0.15), residues: 914 loop : -1.17 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 765 TYR 0.018 0.002 TYR A 170 PHE 0.025 0.002 PHE B 377 TRP 0.043 0.002 TRP B 104 HIS 0.008 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 (30457) covalent geometry : angle 0.71864 / 0.38 (41433) SS BOND : bond 0.00483 / 0.30 ( 43) SS BOND : angle 1.39214 / 0.99 ( 86) hydrogen bonds : bond 0.05300 / 3.45 ( 853) hydrogen bonds : angle 6.65487 / 4.61 ( 2418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 729 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7200 (m) cc_final: 0.6957 (m) REVERT: A 160 TYR cc_start: 0.7142 (p90) cc_final: 0.6826 (p90) REVERT: A 168 PHE cc_start: 0.7489 (t80) cc_final: 0.7107 (t80) REVERT: A 206 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8378 (tptt) REVERT: A 567 ARG cc_start: 0.7297 (mtm180) cc_final: 0.7057 (mtm180) REVERT: A 654 GLU cc_start: 0.8150 (tt0) cc_final: 0.7860 (tt0) REVERT: A 655 TYR cc_start: 0.8888 (t80) cc_final: 0.8639 (t80) REVERT: A 663 ASP cc_start: 0.7559 (m-30) cc_final: 0.7290 (m-30) REVERT: A 752 LEU cc_start: 0.9053 (mt) cc_final: 0.8727 (mt) REVERT: A 776 LYS cc_start: 0.8720 (mttt) cc_final: 0.8433 (ttmm) REVERT: A 914 ASN cc_start: 0.8788 (m-40) cc_final: 0.8469 (m110) REVERT: A 950 ASP cc_start: 0.7788 (t0) cc_final: 0.7552 (t0) REVERT: A 969 LYS cc_start: 0.9092 (mttt) cc_final: 0.8633 (mmmt) REVERT: A 973 ILE cc_start: 0.9010 (tt) cc_final: 0.8223 (pt) REVERT: A 979 ASP cc_start: 0.7888 (m-30) cc_final: 0.7590 (t0) REVERT: A 984 LEU cc_start: 0.8098 (mt) cc_final: 0.7827 (tp) REVERT: A 985 ASP cc_start: 0.8632 (m-30) cc_final: 0.7819 (p0) REVERT: A 986 PRO cc_start: 0.8932 (Cg_exo) cc_final: 0.8683 (Cg_endo) REVERT: A 1002 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8481 (tp40) REVERT: A 1041 ASP cc_start: 0.8306 (m-30) cc_final: 0.7852 (m-30) REVERT: A 1084 ASP cc_start: 0.8145 (p0) cc_final: 0.7581 (t0) REVERT: C 33 THR cc_start: 0.8276 (p) cc_final: 0.8053 (p) REVERT: C 81 ASN cc_start: 0.8747 (t0) cc_final: 0.8335 (m-40) REVERT: C 106 PHE cc_start: 0.7104 (m-10) cc_final: 0.6857 (m-10) REVERT: C 206 LYS cc_start: 0.8731 (tptt) cc_final: 0.8516 (tppt) REVERT: C 287 ASP cc_start: 0.8321 (t0) cc_final: 0.8075 (t0) REVERT: C 389 ASP cc_start: 0.8649 (m-30) cc_final: 0.8272 (p0) REVERT: C 513 LEU cc_start: 0.8126 (pp) cc_final: 0.7637 (pt) REVERT: C 528 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6630 (mmtm) REVERT: C 533 LEU cc_start: 0.8862 (tp) cc_final: 0.8596 (mt) REVERT: C 537 LYS cc_start: 0.9312 (tptt) cc_final: 0.8801 (tptp) REVERT: C 595 VAL cc_start: 0.8540 (t) cc_final: 0.8282 (p) REVERT: C 738 CYS cc_start: 0.6621 (m) cc_final: 0.6418 (m) REVERT: C 765 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7766 (ttp80) REVERT: C 776 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8374 (ttpp) REVERT: C 800 PHE cc_start: 0.6694 (m-10) cc_final: 0.6429 (m-10) REVERT: C 884 SER cc_start: 0.9029 (m) cc_final: 0.8520 (t) REVERT: C 900 MET cc_start: 0.8380 (mmm) cc_final: 0.8100 (mtp) REVERT: C 935 GLN cc_start: 0.8968 (tt0) cc_final: 0.8359 (tm-30) REVERT: C 955 ASN cc_start: 0.8595 (m-40) cc_final: 0.8345 (t0) REVERT: C 957 GLN cc_start: 0.8853 (tt0) cc_final: 0.7891 (tt0) REVERT: C 969 LYS cc_start: 0.9106 (mttt) cc_final: 0.8902 (mtmm) REVERT: C 979 ASP cc_start: 0.8200 (m-30) cc_final: 0.7994 (m-30) REVERT: C 1002 GLN cc_start: 0.8738 (tp40) cc_final: 0.8534 (tp40) REVERT: C 1050 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8079 (ptm) REVERT: C 1116 THR cc_start: 0.8291 (p) cc_final: 0.8007 (p) REVERT: C 1145 LEU cc_start: 0.7874 (mt) cc_final: 0.7641 (mt) REVERT: c 34 MET cc_start: 0.4784 (mmm) cc_final: 0.3817 (mmm) REVERT: B 66 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6690 (t70) REVERT: B 67 VAL cc_start: 0.4220 (OUTLIER) cc_final: 0.3520 (p) REVERT: B 129 LYS cc_start: 0.8352 (tptm) cc_final: 0.8091 (tptm) REVERT: B 141 LEU cc_start: 0.5105 (mt) cc_final: 0.4528 (mp) REVERT: B 195 LYS cc_start: 0.6109 (tptt) cc_final: 0.5875 (tptm) REVERT: B 244 LEU cc_start: 0.6105 (mp) cc_final: 0.4790 (mp) REVERT: B 245 HIS cc_start: 0.7483 (t70) cc_final: 0.7123 (t-90) REVERT: B 258 TRP cc_start: 0.4199 (m100) cc_final: 0.2515 (m-90) REVERT: B 285 ILE cc_start: 0.8723 (mt) cc_final: 0.8287 (pt) REVERT: B 353 TRP cc_start: 0.6668 (p90) cc_final: 0.6192 (p90) REVERT: B 355 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7248 (tpp80) REVERT: B 384 PRO cc_start: 0.8238 (Cg_endo) cc_final: 0.7941 (Cg_exo) REVERT: B 515 PHE cc_start: 0.7286 (m-80) cc_final: 0.6984 (m-80) REVERT: B 581 THR cc_start: 0.8084 (p) cc_final: 0.6762 (m) REVERT: B 595 VAL cc_start: 0.8437 (t) cc_final: 0.8215 (p) REVERT: B 659 SER cc_start: 0.8897 (t) cc_final: 0.8647 (p) REVERT: B 675 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6618 (mm-40) REVERT: B 726 ILE cc_start: 0.9106 (mp) cc_final: 0.8870 (mt) REVERT: B 776 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8585 (ttpp) REVERT: B 782 PHE cc_start: 0.8350 (m-10) cc_final: 0.8122 (m-80) REVERT: B 884 SER cc_start: 0.9112 (m) cc_final: 0.8685 (t) REVERT: B 936 ASP cc_start: 0.8074 (m-30) cc_final: 0.7841 (t0) REVERT: B 969 LYS cc_start: 0.9050 (mttt) cc_final: 0.8809 (mmtt) REVERT: B 1019 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7746 (ttp80) REVERT: B 1043 CYS cc_start: 0.7212 (m) cc_final: 0.7000 (m) REVERT: B 1109 PHE cc_start: 0.5559 (p90) cc_final: 0.4679 (p90) REVERT: B 1116 THR cc_start: 0.7890 (p) cc_final: 0.7647 (p) REVERT: B 1119 ASN cc_start: 0.7903 (m-40) cc_final: 0.7480 (m-40) REVERT: a 23 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8463 (pttp) REVERT: a 31 ARG cc_start: 0.7402 (mmt180) cc_final: 0.7177 (mmm-85) REVERT: a 61 ASN cc_start: 0.7816 (t0) cc_final: 0.7557 (t0) REVERT: a 98 ARG cc_start: 0.6809 (mmm160) cc_final: 0.6220 (tpp80) REVERT: a 142 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4790 (mmm) REVERT: a 153 PHE cc_start: 0.8624 (t80) cc_final: 0.7724 (t80) REVERT: b 143 PHE cc_start: 0.6738 (p90) cc_final: 0.6523 (p90) REVERT: b 170 GLN cc_start: 0.7600 (tp40) cc_final: 0.7187 (tp-100) outliers start: 104 outliers final: 50 residues processed: 793 average time/residue: 0.2003 time to fit residues: 250.7825 Evaluate side-chains 691 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 634 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 142 MET Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 50 LEU Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 188 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A1002 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 314 GLN C1083 HIS B 66 HIS ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.183479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.145143 restraints weight = 69430.189| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 4.41 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30500 Z= 0.142 Angle : 0.587 10.628 41519 Z= 0.304 Chirality : 0.045 0.232 4671 Planarity : 0.004 0.056 5342 Dihedral : 4.846 52.165 4099 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.10 % Allowed : 11.45 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.95 (0.12), residues: 3749 helix: -0.92 (0.19), residues: 620 sheet: 0.40 (0.16), residues: 889 loop : -0.97 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.016 0.001 TYR B1110 PHE 0.023 0.002 PHE B 133 TRP 0.022 0.002 TRP A 886 HIS 0.018 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (30457) covalent geometry : angle 0.58553 / 0.30 (41433) SS BOND : bond 0.00264 / 0.17 ( 43) SS BOND : angle 1.09887 / 0.77 ( 86) hydrogen bonds : bond 0.04512 / 2.99 ( 853) hydrogen bonds : angle 5.92929 / 4.11 ( 2418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 667 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7096 (p90) cc_final: 0.6758 (p90) REVERT: A 168 PHE cc_start: 0.7526 (t80) cc_final: 0.7287 (t80) REVERT: A 206 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8210 (tptp) REVERT: A 224 GLU cc_start: 0.7572 (mp0) cc_final: 0.7281 (mp0) REVERT: A 271 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8191 (mm-40) REVERT: A 592 PHE cc_start: 0.7443 (p90) cc_final: 0.7063 (p90) REVERT: A 655 TYR cc_start: 0.8509 (t80) cc_final: 0.8188 (t80) REVERT: A 663 ASP cc_start: 0.7172 (m-30) cc_final: 0.6894 (m-30) REVERT: A 752 LEU cc_start: 0.8884 (mt) cc_final: 0.8244 (mt) REVERT: A 776 LYS cc_start: 0.8334 (mttt) cc_final: 0.8034 (ttmm) REVERT: A 779 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8005 (tp40) REVERT: A 814 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8290 (mmtt) REVERT: A 868 GLU cc_start: 0.7762 (tt0) cc_final: 0.7551 (tm-30) REVERT: A 914 ASN cc_start: 0.8384 (m-40) cc_final: 0.8039 (m110) REVERT: A 935 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 969 LYS cc_start: 0.8927 (mttt) cc_final: 0.8535 (mmmt) REVERT: A 973 ILE cc_start: 0.8943 (tt) cc_final: 0.8080 (pt) REVERT: A 985 ASP cc_start: 0.8270 (m-30) cc_final: 0.7761 (m-30) REVERT: A 1084 ASP cc_start: 0.7698 (p0) cc_final: 0.7461 (p0) REVERT: A 1110 TYR cc_start: 0.8594 (t80) cc_final: 0.8266 (t80) REVERT: A 1111 GLU cc_start: 0.8324 (tt0) cc_final: 0.7946 (mt-10) REVERT: A 1116 THR cc_start: 0.7811 (p) cc_final: 0.7578 (p) REVERT: C 33 THR cc_start: 0.8061 (p) cc_final: 0.7854 (p) REVERT: C 106 PHE cc_start: 0.7253 (m-80) cc_final: 0.6944 (m-10) REVERT: C 128 ILE cc_start: 0.8074 (mm) cc_final: 0.7550 (mp) REVERT: C 173 GLN cc_start: 0.7054 (pp30) cc_final: 0.6489 (pp30) REVERT: C 287 ASP cc_start: 0.7864 (t0) cc_final: 0.7659 (t0) REVERT: C 315 THR cc_start: 0.7952 (t) cc_final: 0.7611 (t) REVERT: C 353 TRP cc_start: 0.5869 (p90) cc_final: 0.5553 (p90) REVERT: C 389 ASP cc_start: 0.8454 (m-30) cc_final: 0.8034 (p0) REVERT: C 528 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6522 (mmtm) REVERT: C 537 LYS cc_start: 0.8739 (tptt) cc_final: 0.8452 (tptp) REVERT: C 595 VAL cc_start: 0.8542 (t) cc_final: 0.8186 (p) REVERT: C 656 VAL cc_start: 0.8769 (m) cc_final: 0.8545 (p) REVERT: C 765 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7569 (ttp80) REVERT: C 776 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8145 (ttpp) REVERT: C 800 PHE cc_start: 0.6961 (m-10) cc_final: 0.6673 (m-10) REVERT: C 817 PHE cc_start: 0.8171 (t80) cc_final: 0.7701 (t80) REVERT: C 955 ASN cc_start: 0.8313 (m-40) cc_final: 0.8032 (t0) REVERT: C 957 GLN cc_start: 0.8128 (tt0) cc_final: 0.7471 (tt0) REVERT: C 979 ASP cc_start: 0.8014 (m-30) cc_final: 0.7698 (m-30) REVERT: C 1017 GLU cc_start: 0.8238 (tp30) cc_final: 0.7907 (tp30) REVERT: C 1102 TRP cc_start: 0.8685 (m100) cc_final: 0.8483 (m100) REVERT: C 1116 THR cc_start: 0.8046 (p) cc_final: 0.7809 (p) REVERT: c 34 MET cc_start: 0.5067 (mmm) cc_final: 0.4405 (mmm) REVERT: B 67 VAL cc_start: 0.3967 (OUTLIER) cc_final: 0.3526 (m) REVERT: B 129 LYS cc_start: 0.8231 (tptm) cc_final: 0.7872 (tptm) REVERT: B 195 LYS cc_start: 0.5776 (tptt) cc_final: 0.5372 (tptm) REVERT: B 271 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7695 (mm110) REVERT: B 277 LEU cc_start: 0.8830 (mt) cc_final: 0.8616 (mp) REVERT: B 353 TRP cc_start: 0.6040 (p90) cc_final: 0.5765 (p90) REVERT: B 384 PRO cc_start: 0.8255 (Cg_endo) cc_final: 0.8029 (Cg_exo) REVERT: B 386 LYS cc_start: 0.8428 (mttt) cc_final: 0.8151 (mttt) REVERT: B 451 TYR cc_start: 0.5772 (m-10) cc_final: 0.5394 (m-10) REVERT: B 581 THR cc_start: 0.8082 (p) cc_final: 0.6614 (m) REVERT: B 675 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6262 (mm-40) REVERT: B 726 ILE cc_start: 0.9057 (mp) cc_final: 0.8823 (mt) REVERT: B 765 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.7899 (tmm-80) REVERT: B 776 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8504 (ttmm) REVERT: B 814 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8385 (mmmt) REVERT: B 868 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 884 SER cc_start: 0.8942 (m) cc_final: 0.8489 (t) REVERT: B 935 GLN cc_start: 0.7709 (tt0) cc_final: 0.7450 (tm-30) REVERT: B 936 ASP cc_start: 0.8103 (m-30) cc_final: 0.7826 (t0) REVERT: B 950 ASP cc_start: 0.7588 (t0) cc_final: 0.7212 (t0) REVERT: B 954 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.8015 (m-70) REVERT: B 964 LYS cc_start: 0.8744 (mmmm) cc_final: 0.8129 (mmmt) REVERT: B 969 LYS cc_start: 0.8865 (mttt) cc_final: 0.8535 (mtpp) REVERT: B 1019 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7022 (ttp80) REVERT: B 1116 THR cc_start: 0.7682 (p) cc_final: 0.7479 (p) REVERT: B 1119 ASN cc_start: 0.7695 (m-40) cc_final: 0.7285 (m110) REVERT: a 5 GLN cc_start: 0.6901 (tm-30) cc_final: 0.6621 (tm-30) REVERT: a 36 TRP cc_start: 0.7343 (m100) cc_final: 0.7019 (m100) REVERT: a 85 SER cc_start: 0.7671 (t) cc_final: 0.6996 (p) REVERT: a 153 PHE cc_start: 0.8065 (t80) cc_final: 0.7076 (t80) REVERT: a 182 TYR cc_start: 0.6693 (m-80) cc_final: 0.6447 (m-80) REVERT: b 143 PHE cc_start: 0.6473 (p90) cc_final: 0.6259 (p90) REVERT: b 167 TRP cc_start: 0.7114 (p90) cc_final: 0.6893 (p90) REVERT: b 170 GLN cc_start: 0.7423 (tp40) cc_final: 0.7189 (tp-100) outliers start: 103 outliers final: 59 residues processed: 722 average time/residue: 0.1975 time to fit residues: 225.7602 Evaluate side-chains 654 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 591 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 228 optimal weight: 30.0000 chunk 21 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 325 optimal weight: 0.7980 chunk 327 optimal weight: 0.9980 chunk 355 optimal weight: 3.9990 chunk 377 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 422 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.176582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.137460 restraints weight = 68208.024| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.10 r_work: 0.3651 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30500 Z= 0.230 Angle : 0.663 11.646 41519 Z= 0.347 Chirality : 0.047 0.212 4671 Planarity : 0.005 0.060 5342 Dihedral : 5.049 51.337 4099 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 4.01 % Allowed : 11.75 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.73 (0.13), residues: 3749 helix: -0.16 (0.20), residues: 629 sheet: 0.43 (0.16), residues: 930 loop : -0.99 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 567 TYR 0.032 0.002 TYR C 380 PHE 0.042 0.002 PHE C 342 TRP 0.037 0.002 TRP B 104 HIS 0.023 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (30457) covalent geometry : angle 0.66084 / 0.35 (41433) SS BOND : bond 0.00359 / 0.22 ( 43) SS BOND : angle 1.40281 / 0.96 ( 86) hydrogen bonds : bond 0.04554 / 3.04 ( 853) hydrogen bonds : angle 5.70247 / 3.94 ( 2418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 665 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7304 (p90) cc_final: 0.6996 (p90) REVERT: A 169 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8326 (mm-30) REVERT: A 190 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7128 (mtt180) REVERT: A 206 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8393 (tptp) REVERT: A 270 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 606 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8597 (t0) REVERT: A 776 LYS cc_start: 0.8662 (mttt) cc_final: 0.8415 (ttmm) REVERT: A 779 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8141 (tm-30) REVERT: A 823 PHE cc_start: 0.8901 (t80) cc_final: 0.8679 (t80) REVERT: A 868 GLU cc_start: 0.8457 (tt0) cc_final: 0.8092 (tm-30) REVERT: A 872 GLN cc_start: 0.8211 (tt0) cc_final: 0.8008 (tt0) REVERT: A 914 ASN cc_start: 0.8724 (m-40) cc_final: 0.8503 (m-40) REVERT: A 935 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8750 (tm-30) REVERT: A 937 SER cc_start: 0.9064 (m) cc_final: 0.8768 (t) REVERT: A 950 ASP cc_start: 0.7730 (t0) cc_final: 0.7478 (t0) REVERT: A 955 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (t0) REVERT: A 969 LYS cc_start: 0.9218 (mttt) cc_final: 0.8911 (mmtt) REVERT: A 973 ILE cc_start: 0.9036 (tt) cc_final: 0.8767 (pt) REVERT: A 985 ASP cc_start: 0.8450 (m-30) cc_final: 0.8067 (m-30) REVERT: A 1017 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8221 (tm-30) REVERT: A 1084 ASP cc_start: 0.8267 (p0) cc_final: 0.7806 (p0) REVERT: A 1086 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7906 (pttp) REVERT: A 1111 GLU cc_start: 0.8849 (tt0) cc_final: 0.8542 (mt-10) REVERT: C 92 PHE cc_start: 0.8016 (t80) cc_final: 0.7780 (t80) REVERT: C 106 PHE cc_start: 0.7528 (m-80) cc_final: 0.7302 (m-80) REVERT: C 128 ILE cc_start: 0.8494 (mm) cc_final: 0.8257 (mm) REVERT: C 173 GLN cc_start: 0.7322 (pp30) cc_final: 0.6742 (pp30) REVERT: C 201 PHE cc_start: 0.8401 (t80) cc_final: 0.8193 (t80) REVERT: C 275 PHE cc_start: 0.8290 (m-80) cc_final: 0.7976 (m-80) REVERT: C 304 LYS cc_start: 0.9200 (mttt) cc_final: 0.8817 (mmmm) REVERT: C 313 TYR cc_start: 0.8784 (m-80) cc_final: 0.8504 (m-80) REVERT: C 315 THR cc_start: 0.8470 (t) cc_final: 0.8219 (p) REVERT: C 353 TRP cc_start: 0.6534 (p90) cc_final: 0.5662 (p90) REVERT: C 356 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8217 (ttmt) REVERT: C 528 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6913 (mmtm) REVERT: C 537 LYS cc_start: 0.9301 (tptt) cc_final: 0.8982 (tptp) REVERT: C 656 VAL cc_start: 0.8984 (m) cc_final: 0.8758 (p) REVERT: C 765 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7790 (ttp80) REVERT: C 776 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8249 (ttpp) REVERT: C 814 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8458 (mmmt) REVERT: C 816 SER cc_start: 0.8835 (p) cc_final: 0.8239 (t) REVERT: C 884 SER cc_start: 0.8973 (m) cc_final: 0.8491 (t) REVERT: C 957 GLN cc_start: 0.8588 (tt0) cc_final: 0.8048 (tt0) REVERT: C 979 ASP cc_start: 0.8496 (m-30) cc_final: 0.8112 (m-30) REVERT: C 1102 TRP cc_start: 0.8857 (m100) cc_final: 0.8651 (m100) REVERT: C 1139 ASP cc_start: 0.8536 (t0) cc_final: 0.8306 (t0) REVERT: c 34 MET cc_start: 0.4691 (mmm) cc_final: 0.3640 (mmm) REVERT: B 203 ILE cc_start: 0.8921 (mt) cc_final: 0.8690 (pt) REVERT: B 224 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: B 240 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 271 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8376 (mm-40) REVERT: B 277 LEU cc_start: 0.8997 (mt) cc_final: 0.8797 (mp) REVERT: B 386 LYS cc_start: 0.8534 (mttt) cc_final: 0.8243 (mttt) REVERT: B 581 THR cc_start: 0.8855 (p) cc_final: 0.8440 (m) REVERT: B 675 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6991 (mm-40) REVERT: B 726 ILE cc_start: 0.9113 (mp) cc_final: 0.8904 (mt) REVERT: B 737 ASP cc_start: 0.8513 (t0) cc_final: 0.8146 (t0) REVERT: B 739 THR cc_start: 0.8284 (m) cc_final: 0.8029 (p) REVERT: B 765 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.8051 (tmm-80) REVERT: B 776 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8680 (ttmm) REVERT: B 814 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8532 (mmmt) REVERT: B 868 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 884 SER cc_start: 0.9116 (m) cc_final: 0.8636 (t) REVERT: B 935 GLN cc_start: 0.7837 (tt0) cc_final: 0.7545 (tm-30) REVERT: B 936 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 969 LYS cc_start: 0.9073 (mttt) cc_final: 0.8826 (mtpp) REVERT: B 1002 GLN cc_start: 0.8337 (tp40) cc_final: 0.8048 (tp40) REVERT: B 1041 ASP cc_start: 0.8214 (m-30) cc_final: 0.7492 (m-30) REVERT: B 1116 THR cc_start: 0.8115 (p) cc_final: 0.7911 (p) REVERT: B 1119 ASN cc_start: 0.8055 (m-40) cc_final: 0.7679 (m110) REVERT: a 23 LYS cc_start: 0.8940 (pttp) cc_final: 0.8646 (pttp) REVERT: a 36 TRP cc_start: 0.7594 (m100) cc_final: 0.6988 (m100) REVERT: a 85 SER cc_start: 0.7968 (t) cc_final: 0.7405 (p) REVERT: a 153 PHE cc_start: 0.8634 (t80) cc_final: 0.7491 (t80) REVERT: a 154 PRO cc_start: 0.8824 (Cg_endo) cc_final: 0.8580 (Cg_exo) outliers start: 133 outliers final: 88 residues processed: 734 average time/residue: 0.1952 time to fit residues: 228.6735 Evaluate side-chains 713 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 616 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 17 optimal weight: 0.0170 chunk 376 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 28 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.0296 > 50:) overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 616 ASN A 755 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 207 HIS C 914 ASN B 895 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** a 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.177866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.138882 restraints weight = 68448.632| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.14 r_work: 0.3668 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30500 Z= 0.123 Angle : 0.584 10.897 41519 Z= 0.300 Chirality : 0.044 0.190 4671 Planarity : 0.004 0.060 5342 Dihedral : 4.740 51.277 4097 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 3.40 % Allowed : 14.49 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.45 (0.13), residues: 3749 helix: 0.50 (0.22), residues: 618 sheet: 0.51 (0.16), residues: 904 loop : -0.88 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.026 0.001 TYR B 421 PHE 0.035 0.002 PHE B 192 TRP 0.022 0.001 TRP B 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (30457) covalent geometry : angle 0.58274 / 0.30 (41433) SS BOND : bond 0.00225 / 0.13 ( 43) SS BOND : angle 1.10415 / 0.82 ( 86) hydrogen bonds : bond 0.03886 / 2.61 ( 853) hydrogen bonds : angle 5.38097 / 3.74 ( 2418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 627 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: 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 138 ASP cc_start: 0.8318 (t0) cc_final: 0.7958 (t0) REVERT: A 160 TYR cc_start: 0.7238 (p90) cc_final: 0.6855 (p90) REVERT: A 190 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7073 (mtt180) REVERT: A 206 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8439 (tptp) REVERT: A 221 SER cc_start: 0.8734 (t) cc_final: 0.8381 (p) REVERT: A 298 GLU cc_start: 0.8520 (tp30) cc_final: 0.8167 (tp30) REVERT: A 606 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8801 (t0) REVERT: A 608 VAL cc_start: 0.8904 (t) cc_final: 0.8662 (m) REVERT: A 616 ASN cc_start: 0.6851 (m-40) cc_final: 0.6601 (m-40) REVERT: A 655 TYR cc_start: 0.8421 (t80) cc_final: 0.7920 (t80) REVERT: A 776 LYS cc_start: 0.8587 (mttt) cc_final: 0.8326 (ttmm) REVERT: A 779 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8141 (tm-30) REVERT: A 823 PHE cc_start: 0.8898 (t80) cc_final: 0.8648 (t80) REVERT: A 868 GLU cc_start: 0.8320 (tt0) cc_final: 0.8020 (tm-30) REVERT: A 914 ASN cc_start: 0.8724 (m-40) cc_final: 0.8461 (m-40) REVERT: A 935 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8793 (tm-30) REVERT: A 937 SER cc_start: 0.8996 (m) cc_final: 0.8719 (t) REVERT: A 955 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 964 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8673 (mmmt) REVERT: A 969 LYS cc_start: 0.9241 (mttt) cc_final: 0.8890 (mmtt) REVERT: A 973 ILE cc_start: 0.9056 (tt) cc_final: 0.8785 (pt) REVERT: A 1017 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 1045 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8409 (tptp) REVERT: A 1084 ASP cc_start: 0.8318 (p0) cc_final: 0.7946 (p0) REVERT: A 1107 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7620 (mtt90) REVERT: A 1110 TYR cc_start: 0.8888 (t80) cc_final: 0.8580 (t80) REVERT: A 1111 GLU cc_start: 0.8834 (tt0) cc_final: 0.8575 (mt-10) REVERT: C 81 ASN cc_start: 0.8710 (m-40) cc_final: 0.8488 (m-40) REVERT: C 92 PHE cc_start: 0.8003 (t80) cc_final: 0.7679 (t80) REVERT: C 106 PHE cc_start: 0.7382 (m-80) cc_final: 0.7086 (m-80) REVERT: C 128 ILE cc_start: 0.8411 (mm) cc_final: 0.7999 (mp) REVERT: C 173 GLN cc_start: 0.7384 (pp30) cc_final: 0.6848 (pp30) REVERT: C 220 PHE cc_start: 0.7974 (t80) cc_final: 0.7478 (t80) REVERT: C 275 PHE cc_start: 0.8171 (m-80) cc_final: 0.7768 (m-80) REVERT: C 287 ASP cc_start: 0.8474 (t0) cc_final: 0.8173 (t0) REVERT: C 290 ASP cc_start: 0.8507 (t0) cc_final: 0.8154 (t0) REVERT: C 304 LYS cc_start: 0.9199 (mttt) cc_final: 0.8845 (mmmm) REVERT: C 313 TYR cc_start: 0.8760 (m-80) cc_final: 0.8541 (m-80) REVERT: C 355 ARG cc_start: 0.7677 (mpt-90) cc_final: 0.7392 (mpt-90) REVERT: C 357 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8100 (tmm160) REVERT: C 389 ASP cc_start: 0.8811 (m-30) cc_final: 0.8486 (p0) REVERT: C 537 LYS cc_start: 0.9265 (tptt) cc_final: 0.9038 (tptp) REVERT: C 656 VAL cc_start: 0.8842 (m) cc_final: 0.8587 (p) REVERT: C 775 ASP cc_start: 0.8281 (m-30) cc_final: 0.7785 (t0) REVERT: C 776 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8344 (ttpp) REVERT: C 816 SER cc_start: 0.8735 (p) cc_final: 0.8351 (t) REVERT: C 884 SER cc_start: 0.8984 (m) cc_final: 0.8565 (t) REVERT: C 895 GLN cc_start: 0.7329 (tp40) cc_final: 0.7068 (tp40) REVERT: C 957 GLN cc_start: 0.8534 (tt0) cc_final: 0.8020 (tt0) REVERT: C 979 ASP cc_start: 0.8514 (m-30) cc_final: 0.8095 (m-30) REVERT: C 1002 GLN cc_start: 0.8568 (tp40) cc_final: 0.7871 (tm-30) REVERT: C 1006 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8804 (t) REVERT: C 1102 TRP cc_start: 0.8848 (m100) cc_final: 0.8607 (m100) REVERT: C 1111 GLU cc_start: 0.8212 (pt0) cc_final: 0.7925 (pm20) REVERT: C 1139 ASP cc_start: 0.8482 (t0) cc_final: 0.8180 (t0) REVERT: c 34 MET cc_start: 0.4711 (mmm) cc_final: 0.3645 (mmm) REVERT: B 79 PHE cc_start: 0.7640 (m-80) cc_final: 0.7370 (m-80) REVERT: B 191 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7412 (mp0) REVERT: B 195 LYS cc_start: 0.6376 (tptt) cc_final: 0.5289 (tppt) REVERT: B 203 ILE cc_start: 0.8898 (mt) cc_final: 0.8651 (pt) REVERT: B 224 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: B 271 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8311 (mm110) REVERT: B 276 LEU cc_start: 0.8922 (tp) cc_final: 0.8685 (tt) REVERT: B 277 LEU cc_start: 0.8984 (mt) cc_final: 0.8775 (mp) REVERT: B 304 LYS cc_start: 0.8994 (mttt) cc_final: 0.8751 (mmtt) REVERT: B 329 PHE cc_start: 0.5951 (m-80) cc_final: 0.5741 (m-80) REVERT: B 351 TYR cc_start: 0.8173 (p90) cc_final: 0.7436 (p90) REVERT: B 353 TRP cc_start: 0.6538 (p90) cc_final: 0.6161 (p90) REVERT: B 509 ARG cc_start: 0.5041 (mmt180) cc_final: 0.4552 (mmm160) REVERT: B 581 THR cc_start: 0.8583 (p) cc_final: 0.8019 (m) REVERT: B 675 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7081 (mm-40) REVERT: B 737 ASP cc_start: 0.8488 (t0) cc_final: 0.8265 (t70) REVERT: B 765 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8041 (tmm-80) REVERT: B 776 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8722 (ttmm) REVERT: B 814 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8500 (mmmt) REVERT: B 819 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 868 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 884 SER cc_start: 0.9107 (m) cc_final: 0.8653 (t) REVERT: B 935 GLN cc_start: 0.7825 (tt0) cc_final: 0.7542 (tm-30) REVERT: B 954 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8198 (m170) REVERT: B 969 LYS cc_start: 0.9070 (mttt) cc_final: 0.8804 (mtpp) REVERT: B 1041 ASP cc_start: 0.7998 (m-30) cc_final: 0.7683 (m-30) REVERT: B 1045 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7922 (mmmm) REVERT: B 1119 ASN cc_start: 0.7945 (m-40) cc_final: 0.7583 (m110) REVERT: a 5 GLN cc_start: 0.7256 (pp30) cc_final: 0.6797 (pp30) REVERT: a 34 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (mpp) REVERT: a 36 TRP cc_start: 0.7494 (m100) cc_final: 0.7205 (m100) REVERT: a 39 GLN cc_start: 0.8456 (tp40) cc_final: 0.8213 (tp40) REVERT: a 85 SER cc_start: 0.7980 (t) cc_final: 0.7442 (p) REVERT: a 153 PHE cc_start: 0.8597 (t80) cc_final: 0.7398 (t80) REVERT: a 154 PRO cc_start: 0.8743 (Cg_endo) cc_final: 0.8501 (Cg_exo) outliers start: 113 outliers final: 77 residues processed: 684 average time/residue: 0.1996 time to fit residues: 216.5268 Evaluate side-chains 695 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 611 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 184 LEU Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 49 LYS Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 152 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 1 optimal weight: 0.7980 chunk 332 optimal weight: 0.4980 chunk 288 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 260 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 544 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.177245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.137824 restraints weight = 68265.289| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 4.14 r_work: 0.3660 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30500 Z= 0.130 Angle : 0.572 10.026 41519 Z= 0.293 Chirality : 0.044 0.193 4671 Planarity : 0.004 0.056 5342 Dihedral : 4.626 54.451 4097 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 3.46 % Allowed : 15.00 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.36 (0.13), residues: 3749 helix: 0.75 (0.22), residues: 622 sheet: 0.54 (0.17), residues: 899 loop : -0.87 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 567 TYR 0.024 0.001 TYR C 365 PHE 0.035 0.002 PHE C 342 TRP 0.022 0.001 TRP B 104 HIS 0.031 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (30457) covalent geometry : angle 0.57123 / 0.29 (41433) SS BOND : bond 0.00231 / 0.13 ( 43) SS BOND : angle 0.99747 / 0.72 ( 86) hydrogen bonds : bond 0.03701 / 2.47 ( 853) hydrogen bonds : angle 5.20615 / 3.61 ( 2418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 629 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8331 (t0) cc_final: 0.7985 (t0) REVERT: A 160 TYR cc_start: 0.7246 (p90) cc_final: 0.6887 (p90) REVERT: A 206 LYS cc_start: 0.8929 (tmtt) cc_final: 0.8481 (tptp) REVERT: A 221 SER cc_start: 0.8737 (t) cc_final: 0.8376 (p) REVERT: A 606 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8602 (t0) REVERT: A 608 VAL cc_start: 0.8934 (t) cc_final: 0.8704 (m) REVERT: A 655 TYR cc_start: 0.8366 (t80) cc_final: 0.7904 (t80) REVERT: A 776 LYS cc_start: 0.8577 (mttt) cc_final: 0.8314 (ttmm) REVERT: A 779 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8080 (tm-30) REVERT: A 823 PHE cc_start: 0.8889 (t80) cc_final: 0.8617 (t80) REVERT: A 868 GLU cc_start: 0.8377 (tt0) cc_final: 0.8014 (tm-30) REVERT: A 869 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: A 914 ASN cc_start: 0.8722 (m-40) cc_final: 0.8494 (m-40) REVERT: A 937 SER cc_start: 0.9024 (m) cc_final: 0.8739 (t) REVERT: A 955 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8378 (t0) REVERT: A 964 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8791 (mmmt) REVERT: A 969 LYS cc_start: 0.9239 (mttt) cc_final: 0.8888 (mmtt) REVERT: A 973 ILE cc_start: 0.9070 (tt) cc_final: 0.8744 (pt) REVERT: A 1017 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 1084 ASP cc_start: 0.8372 (p0) cc_final: 0.7986 (p0) REVERT: A 1110 TYR cc_start: 0.8929 (t80) cc_final: 0.8595 (t80) REVERT: A 1111 GLU cc_start: 0.8795 (tt0) cc_final: 0.8588 (mt-10) REVERT: C 92 PHE cc_start: 0.8027 (t80) cc_final: 0.7709 (t80) REVERT: C 106 PHE cc_start: 0.7237 (m-80) cc_final: 0.6974 (m-80) REVERT: C 173 GLN cc_start: 0.7408 (pp30) cc_final: 0.6804 (pp30) REVERT: C 220 PHE cc_start: 0.7994 (t80) cc_final: 0.7485 (t80) REVERT: C 275 PHE cc_start: 0.8230 (m-10) cc_final: 0.7931 (m-80) REVERT: C 287 ASP cc_start: 0.8491 (t0) cc_final: 0.8194 (t0) REVERT: C 290 ASP cc_start: 0.8542 (t0) cc_final: 0.8288 (t70) REVERT: C 298 GLU cc_start: 0.8759 (tp30) cc_final: 0.8533 (tp30) REVERT: C 304 LYS cc_start: 0.9208 (mttt) cc_final: 0.8835 (mmmm) REVERT: C 313 TYR cc_start: 0.8749 (m-80) cc_final: 0.8532 (m-80) REVERT: C 355 ARG cc_start: 0.7613 (mpt-90) cc_final: 0.7389 (mpt-90) REVERT: C 356 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7950 (ttmt) REVERT: C 498 ARG cc_start: 0.5898 (ptt-90) cc_final: 0.5393 (ptt-90) REVERT: C 537 LYS cc_start: 0.9247 (tptt) cc_final: 0.8898 (tptm) REVERT: C 643 PHE cc_start: 0.8242 (t80) cc_final: 0.8033 (t80) REVERT: C 656 VAL cc_start: 0.8861 (m) cc_final: 0.8544 (p) REVERT: C 775 ASP cc_start: 0.8277 (m-30) cc_final: 0.7824 (t0) REVERT: C 776 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8250 (ttpp) REVERT: C 814 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8440 (mmmt) REVERT: C 816 SER cc_start: 0.8706 (p) cc_final: 0.8355 (t) REVERT: C 817 PHE cc_start: 0.8727 (t80) cc_final: 0.8374 (t80) REVERT: C 884 SER cc_start: 0.8984 (m) cc_final: 0.8589 (t) REVERT: C 918 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8214 (mp0) REVERT: C 957 GLN cc_start: 0.8510 (tt0) cc_final: 0.7979 (tt0) REVERT: C 979 ASP cc_start: 0.8494 (m-30) cc_final: 0.8146 (m-30) REVERT: C 1002 GLN cc_start: 0.8514 (tp40) cc_final: 0.7822 (tm-30) REVERT: C 1006 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (t) REVERT: C 1073 LYS cc_start: 0.8752 (mttt) cc_final: 0.8401 (mttm) REVERT: C 1102 TRP cc_start: 0.8850 (m100) cc_final: 0.7824 (m100) REVERT: C 1111 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: C 1139 ASP cc_start: 0.8472 (t0) cc_final: 0.8145 (t0) REVERT: c 34 MET cc_start: 0.4704 (mmm) cc_final: 0.3640 (mmm) REVERT: B 79 PHE cc_start: 0.7716 (m-80) cc_final: 0.7389 (m-80) REVERT: B 195 LYS cc_start: 0.6580 (tptt) cc_final: 0.5408 (tppt) REVERT: B 203 ILE cc_start: 0.8877 (mt) cc_final: 0.8636 (pt) REVERT: B 206 LYS cc_start: 0.8035 (tppt) cc_final: 0.7493 (tptp) REVERT: B 224 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: B 271 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8310 (mm110) REVERT: B 276 LEU cc_start: 0.8913 (tp) cc_final: 0.8675 (tt) REVERT: B 304 LYS cc_start: 0.9019 (mttt) cc_final: 0.8756 (mmtt) REVERT: B 356 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7192 (ttpt) REVERT: B 581 THR cc_start: 0.8643 (p) cc_final: 0.8103 (m) REVERT: B 675 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7023 (mm-40) REVERT: B 742 ILE cc_start: 0.9272 (mm) cc_final: 0.9043 (mt) REVERT: B 765 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.8015 (tmm-80) REVERT: B 776 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8706 (ttmm) REVERT: B 805 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8165 (tp) REVERT: B 814 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8566 (mmmt) REVERT: B 868 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 884 SER cc_start: 0.9131 (m) cc_final: 0.8742 (t) REVERT: B 933 LYS cc_start: 0.8539 (mttt) cc_final: 0.8239 (mttt) REVERT: B 954 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8204 (m170) REVERT: B 969 LYS cc_start: 0.9057 (mttt) cc_final: 0.8795 (mttm) REVERT: B 1029 MET cc_start: 0.8920 (tpp) cc_final: 0.8645 (tpp) REVERT: B 1041 ASP cc_start: 0.8001 (m-30) cc_final: 0.7660 (m-30) REVERT: B 1045 LYS cc_start: 0.8562 (mmmm) cc_final: 0.7957 (mmmm) REVERT: B 1119 ASN cc_start: 0.7944 (m-40) cc_final: 0.7594 (m110) REVERT: a 5 GLN cc_start: 0.6929 (pp30) cc_final: 0.6455 (pm20) REVERT: a 31 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7202 (mmm-85) REVERT: a 34 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8150 (mpp) REVERT: a 36 TRP cc_start: 0.7446 (m100) cc_final: 0.7167 (m100) REVERT: a 39 GLN cc_start: 0.8450 (tp40) cc_final: 0.8180 (tp40) REVERT: a 85 SER cc_start: 0.7996 (t) cc_final: 0.7475 (p) REVERT: a 93 VAL cc_start: 0.8353 (t) cc_final: 0.8147 (p) REVERT: a 98 ARG cc_start: 0.6876 (mmm160) cc_final: 0.6175 (tpp80) REVERT: a 153 PHE cc_start: 0.8571 (t80) cc_final: 0.7427 (t80) REVERT: a 154 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8420 (Cg_exo) REVERT: b 143 PHE cc_start: 0.6793 (p90) cc_final: 0.6503 (p90) REVERT: b 170 GLN cc_start: 0.8039 (tp40) cc_final: 0.6986 (tm-30) outliers start: 115 outliers final: 77 residues processed: 687 average time/residue: 0.2026 time to fit residues: 220.1762 Evaluate side-chains 701 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 614 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain c residue 102 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 34 MET Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 43 LYS Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 107 LYS Chi-restraints excluded: chain b residue 152 TRP Chi-restraints excluded: chain b residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 81 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C1106 GLN B 122 ASN B1074 ASN B1113 GLN a 5 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.175149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135539 restraints weight = 67923.142| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.13 r_work: 0.3624 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30500 Z= 0.162 Angle : 0.602 10.674 41519 Z= 0.308 Chirality : 0.045 0.176 4671 Planarity : 0.004 0.054 5342 Dihedral : 4.626 58.588 4094 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.46 % Allowed : 15.64 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.42 (0.13), residues: 3749 helix: 0.73 (0.22), residues: 627 sheet: 0.49 (0.17), residues: 894 loop : -0.92 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.020 0.001 TYR B 421 PHE 0.026 0.002 PHE C 55 TRP 0.041 0.002 TRP B 104 HIS 0.022 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (30457) covalent geometry : angle 0.59967 / 0.31 (41433) SS BOND : bond 0.00317 / 0.23 ( 43) SS BOND : angle 1.40857 / 1.07 ( 86) hydrogen bonds : bond 0.03828 / 2.56 ( 853) hydrogen bonds : angle 5.19769 / 3.59 ( 2418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 628 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8357 (t0) cc_final: 0.8041 (t0) REVERT: A 160 TYR cc_start: 0.7270 (p90) cc_final: 0.7007 (p90) REVERT: A 206 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8507 (tptp) REVERT: A 221 SER cc_start: 0.8782 (t) cc_final: 0.8400 (p) REVERT: A 298 GLU cc_start: 0.8674 (tp30) cc_final: 0.8081 (tt0) REVERT: A 314 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 564 GLN cc_start: 0.8627 (tt0) cc_final: 0.8205 (mm-40) REVERT: A 606 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8619 (t0) REVERT: A 608 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8732 (m) REVERT: A 655 TYR cc_start: 0.8394 (t80) cc_final: 0.8048 (t80) REVERT: A 750 SER cc_start: 0.8920 (m) cc_final: 0.8615 (t) REVERT: A 776 LYS cc_start: 0.8551 (mttt) cc_final: 0.8306 (ttmm) REVERT: A 779 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8067 (tm-30) REVERT: A 823 PHE cc_start: 0.8914 (t80) cc_final: 0.8645 (t80) REVERT: A 868 GLU cc_start: 0.8429 (tt0) cc_final: 0.8049 (tm-30) REVERT: A 914 ASN cc_start: 0.8749 (m-40) cc_final: 0.8501 (m-40) REVERT: A 937 SER cc_start: 0.9031 (m) cc_final: 0.8752 (t) REVERT: A 955 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8390 (t0) REVERT: A 964 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8852 (mmmt) REVERT: A 969 LYS cc_start: 0.9219 (mttt) cc_final: 0.8741 (mtpp) REVERT: A 980 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 988 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8197 (tp30) REVERT: A 1017 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 1072 GLU cc_start: 0.8634 (pm20) cc_final: 0.8060 (mp0) REVERT: A 1084 ASP cc_start: 0.8423 (p0) cc_final: 0.7984 (p0) REVERT: A 1110 TYR cc_start: 0.8993 (t80) cc_final: 0.8551 (t80) REVERT: C 92 PHE cc_start: 0.8038 (t80) cc_final: 0.7724 (t80) REVERT: C 106 PHE cc_start: 0.7460 (m-80) cc_final: 0.7255 (m-80) REVERT: C 173 GLN cc_start: 0.7409 (pp30) cc_final: 0.6827 (pp30) REVERT: C 189 LEU cc_start: 0.8317 (tp) cc_final: 0.7756 (pp) REVERT: C 204 TYR cc_start: 0.7916 (m-80) cc_final: 0.7283 (m-80) REVERT: C 206 LYS cc_start: 0.8604 (tptt) cc_final: 0.8296 (tptt) REVERT: C 220 PHE cc_start: 0.8057 (t80) cc_final: 0.7464 (t80) REVERT: C 237 ARG cc_start: 0.7679 (mtm180) cc_final: 0.7271 (mtm180) REVERT: C 275 PHE cc_start: 0.8239 (m-10) cc_final: 0.7930 (m-80) REVERT: C 290 ASP cc_start: 0.8558 (t0) cc_final: 0.8338 (t70) REVERT: C 298 GLU cc_start: 0.8761 (tp30) cc_final: 0.8521 (tp30) REVERT: C 304 LYS cc_start: 0.9209 (mttt) cc_final: 0.8878 (mmmm) REVERT: C 313 TYR cc_start: 0.8671 (m-80) cc_final: 0.8406 (m-80) REVERT: C 355 ARG cc_start: 0.7597 (mpt-90) cc_final: 0.7380 (mpt-90) REVERT: C 498 ARG cc_start: 0.6270 (ptt-90) cc_final: 0.5563 (ptt-90) REVERT: C 537 LYS cc_start: 0.9118 (tptt) cc_final: 0.8881 (tptm) REVERT: C 656 VAL cc_start: 0.8801 (m) cc_final: 0.8455 (p) REVERT: C 748 GLU cc_start: 0.8337 (pt0) cc_final: 0.7967 (pt0) REVERT: C 775 ASP cc_start: 0.8316 (m-30) cc_final: 0.7894 (t0) REVERT: C 814 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8608 (mmmt) REVERT: C 816 SER cc_start: 0.8793 (p) cc_final: 0.8461 (t) REVERT: C 820 ASP cc_start: 0.8791 (t0) cc_final: 0.8496 (m-30) REVERT: C 884 SER cc_start: 0.8990 (m) cc_final: 0.8525 (t) REVERT: C 918 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8190 (mp0) REVERT: C 957 GLN cc_start: 0.8524 (tt0) cc_final: 0.8013 (tt0) REVERT: C 1002 GLN cc_start: 0.8522 (tp40) cc_final: 0.7819 (tm-30) REVERT: C 1006 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8817 (t) REVERT: C 1073 LYS cc_start: 0.8745 (mttt) cc_final: 0.8433 (mttm) REVERT: C 1102 TRP cc_start: 0.8880 (m100) cc_final: 0.7834 (m100) REVERT: C 1139 ASP cc_start: 0.8533 (t0) cc_final: 0.8239 (t0) REVERT: c 34 MET cc_start: 0.4695 (mmm) cc_final: 0.3650 (mmm) REVERT: B 79 PHE cc_start: 0.7797 (m-80) cc_final: 0.7441 (m-80) REVERT: B 192 PHE cc_start: 0.7816 (m-10) cc_final: 0.7593 (m-10) REVERT: B 203 ILE cc_start: 0.8904 (mt) cc_final: 0.8663 (pt) REVERT: B 206 LYS cc_start: 0.8072 (tppt) cc_final: 0.7606 (tptp) REVERT: B 224 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: B 237 ARG cc_start: 0.7439 (mtt-85) cc_final: 0.7041 (mpp80) REVERT: B 240 THR cc_start: 0.8642 (m) cc_final: 0.8314 (t) REVERT: B 351 TYR cc_start: 0.8307 (p90) cc_final: 0.7570 (p90) REVERT: B 356 LYS cc_start: 0.7539 (ttmt) cc_final: 0.7327 (mtmt) REVERT: B 508 TYR cc_start: 0.7192 (m-80) cc_final: 0.6828 (m-80) REVERT: B 675 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7056 (mm-40) REVERT: B 742 ILE cc_start: 0.9280 (mm) cc_final: 0.9047 (mt) REVERT: B 764 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8694 (ttmm) REVERT: B 765 ARG cc_start: 0.8473 (tmm-80) cc_final: 0.8041 (tmm-80) REVERT: B 776 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8839 (ttpp) REVERT: B 804 GLN cc_start: 0.8767 (tp40) cc_final: 0.8443 (mt0) REVERT: B 805 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 814 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8529 (mmmt) REVERT: B 868 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 884 SER cc_start: 0.9186 (m) cc_final: 0.8816 (t) REVERT: B 933 LYS cc_start: 0.8513 (mttt) cc_final: 0.8231 (mttt) REVERT: B 935 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 954 HIS cc_start: 0.8611 (m-70) cc_final: 0.8280 (m170) REVERT: B 969 LYS cc_start: 0.9061 (mttt) cc_final: 0.8794 (mttm) REVERT: B 1029 MET cc_start: 0.8935 (tpp) cc_final: 0.8648 (tpp) REVERT: B 1084 ASP cc_start: 0.8943 (t0) cc_final: 0.8650 (t0) REVERT: B 1118 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7522 (p0) REVERT: B 1119 ASN cc_start: 0.8045 (m-40) cc_final: 0.7655 (m110) REVERT: a 5 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: a 31 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: a 36 TRP cc_start: 0.7515 (m100) cc_final: 0.7081 (m100) REVERT: a 57 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7896 (tt0) REVERT: a 85 SER cc_start: 0.8007 (t) cc_final: 0.7474 (p) REVERT: a 93 VAL cc_start: 0.8377 (t) cc_final: 0.8162 (p) REVERT: a 98 ARG cc_start: 0.7169 (mmm160) cc_final: 0.6330 (tpp80) REVERT: a 153 PHE cc_start: 0.8650 (t80) cc_final: 0.7548 (t80) REVERT: a 154 PRO cc_start: 0.8686 (Cg_endo) cc_final: 0.8427 (Cg_exo) REVERT: b 143 PHE cc_start: 0.6746 (p90) cc_final: 0.6425 (p90) REVERT: b 170 GLN cc_start: 0.8113 (tp40) cc_final: 0.7188 (tm-30) REVERT: b 179 MET cc_start: 0.3705 (tpp) cc_final: 0.3454 (tpp) outliers start: 115 outliers final: 82 residues processed: 687 average time/residue: 0.1982 time to fit residues: 214.6860 Evaluate side-chains 704 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 612 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain c residue 101 TYR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain a residue 5 GLN Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 73 THR Chi-restraints excluded: chain b residue 152 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 347 optimal weight: 0.9990 chunk 351 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 288 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 185 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 242 optimal weight: 0.0970 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 314 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN C 935 GLN B1113 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.175902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.136783 restraints weight = 68025.946| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 4.09 r_work: 0.3638 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30500 Z= 0.131 Angle : 0.600 13.376 41519 Z= 0.304 Chirality : 0.044 0.168 4671 Planarity : 0.004 0.056 5342 Dihedral : 4.580 58.984 4094 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.34 % Allowed : 16.12 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.37 (0.13), residues: 3749 helix: 0.78 (0.22), residues: 624 sheet: 0.44 (0.17), residues: 918 loop : -0.85 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 567 TYR 0.032 0.001 TYR C 365 PHE 0.042 0.002 PHE b 75 TRP 0.033 0.001 TRP B 104 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (30457) covalent geometry : angle 0.59664 / 0.30 (41433) SS BOND : bond 0.00302 / 0.17 ( 43) SS BOND : angle 1.54092 / 1.16 ( 86) hydrogen bonds : bond 0.03600 / 2.42 ( 853) hydrogen bonds : angle 5.08336 / 3.51 ( 2418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 622 time to evaluate : 0.958 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 138 ASP cc_start: 0.8335 (t0) cc_final: 0.8005 (t0) REVERT: A 160 TYR cc_start: 0.7169 (p90) cc_final: 0.6875 (p90) REVERT: A 190 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7216 (mtt180) REVERT: A 206 LYS cc_start: 0.8930 (tmtt) cc_final: 0.8485 (tptp) REVERT: A 221 SER cc_start: 0.8778 (t) cc_final: 0.8412 (p) REVERT: A 298 GLU cc_start: 0.8635 (tp30) cc_final: 0.7999 (tm-30) REVERT: A 564 GLN cc_start: 0.8670 (tt0) cc_final: 0.8264 (mm-40) REVERT: A 606 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8620 (t0) REVERT: A 608 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 750 SER cc_start: 0.8877 (m) cc_final: 0.8576 (t) REVERT: A 776 LYS cc_start: 0.8546 (mttt) cc_final: 0.8295 (ttmm) REVERT: A 779 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8052 (tm-30) REVERT: A 823 PHE cc_start: 0.8911 (t80) cc_final: 0.8613 (t80) REVERT: A 868 GLU cc_start: 0.8371 (tt0) cc_final: 0.8000 (tm-30) REVERT: A 914 ASN cc_start: 0.8715 (m-40) cc_final: 0.8498 (m-40) REVERT: A 937 SER cc_start: 0.9028 (m) cc_final: 0.8733 (t) REVERT: A 955 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 969 LYS cc_start: 0.9222 (mttt) cc_final: 0.8727 (mtpp) REVERT: A 988 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8163 (tp30) REVERT: A 1002 GLN cc_start: 0.8593 (tp40) cc_final: 0.8218 (mm-40) REVERT: A 1017 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 1072 GLU cc_start: 0.8643 (pm20) cc_final: 0.8117 (mp0) REVERT: A 1084 ASP cc_start: 0.8431 (p0) cc_final: 0.8011 (p0) REVERT: A 1110 TYR cc_start: 0.8995 (t80) cc_final: 0.8570 (t80) REVERT: C 106 PHE cc_start: 0.7476 (m-80) cc_final: 0.7208 (m-80) REVERT: C 173 GLN cc_start: 0.7360 (pp30) cc_final: 0.6792 (pp30) REVERT: C 189 LEU cc_start: 0.8383 (tp) cc_final: 0.7803 (pp) REVERT: C 204 TYR cc_start: 0.7805 (m-80) cc_final: 0.7246 (m-80) REVERT: C 237 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7189 (mtm110) REVERT: C 240 THR cc_start: 0.8081 (m) cc_final: 0.7607 (t) REVERT: C 287 ASP cc_start: 0.8469 (t0) cc_final: 0.8184 (t0) REVERT: C 290 ASP cc_start: 0.8559 (t0) cc_final: 0.8347 (t70) REVERT: C 304 LYS cc_start: 0.9210 (mttt) cc_final: 0.8891 (mmmm) REVERT: C 313 TYR cc_start: 0.8673 (m-80) cc_final: 0.8429 (m-80) REVERT: C 357 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8299 (tmm160) REVERT: C 389 ASP cc_start: 0.8780 (m-30) cc_final: 0.8495 (p0) REVERT: C 498 ARG cc_start: 0.6243 (ptt-90) cc_final: 0.5441 (ptt-90) REVERT: C 537 LYS cc_start: 0.9279 (tptt) cc_final: 0.8926 (tptm) REVERT: C 610 VAL cc_start: 0.9041 (t) cc_final: 0.8634 (m) REVERT: C 656 VAL cc_start: 0.8848 (m) cc_final: 0.8630 (m) REVERT: C 710 ASN cc_start: 0.8430 (m110) cc_final: 0.8070 (p0) REVERT: C 775 ASP cc_start: 0.8294 (m-30) cc_final: 0.7939 (t0) REVERT: C 814 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8616 (mmmt) REVERT: C 816 SER cc_start: 0.8789 (p) cc_final: 0.8500 (t) REVERT: C 820 ASP cc_start: 0.8779 (t0) cc_final: 0.8473 (m-30) REVERT: C 884 SER cc_start: 0.8999 (m) cc_final: 0.8547 (t) REVERT: C 921 LYS cc_start: 0.9141 (mttt) cc_final: 0.8869 (mttt) REVERT: C 957 GLN cc_start: 0.8567 (tt0) cc_final: 0.7994 (tt0) REVERT: C 1002 GLN cc_start: 0.8369 (tp40) cc_final: 0.7816 (tm-30) REVERT: C 1006 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8806 (t) REVERT: C 1073 LYS cc_start: 0.8780 (mttt) cc_final: 0.8471 (mttm) REVERT: C 1102 TRP cc_start: 0.8877 (m100) cc_final: 0.7903 (m100) REVERT: C 1139 ASP cc_start: 0.8509 (t0) cc_final: 0.8200 (t0) REVERT: c 34 MET cc_start: 0.4666 (mmm) cc_final: 0.3635 (mmm) REVERT: B 79 PHE cc_start: 0.7717 (m-80) cc_final: 0.7415 (m-80) REVERT: B 190 ARG cc_start: 0.6671 (ttm-80) cc_final: 0.6287 (ttt180) REVERT: B 203 ILE cc_start: 0.8899 (mt) cc_final: 0.8604 (pt) REVERT: B 206 LYS cc_start: 0.8154 (tppt) cc_final: 0.7692 (tptp) REVERT: B 224 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: B 237 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.7072 (mpp80) REVERT: B 276 LEU cc_start: 0.8880 (tp) cc_final: 0.8579 (tt) REVERT: B 351 TYR cc_start: 0.8305 (p90) cc_final: 0.7579 (p90) REVERT: B 508 TYR cc_start: 0.7110 (m-80) cc_final: 0.6819 (m-80) REVERT: B 675 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7022 (mm-40) REVERT: B 742 ILE cc_start: 0.9279 (mm) cc_final: 0.9036 (mt) REVERT: B 765 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.7874 (ttp80) REVERT: B 776 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8846 (ttpp) REVERT: B 805 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8301 (tp) REVERT: B 868 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 884 SER cc_start: 0.9190 (m) cc_final: 0.8814 (t) REVERT: B 933 LYS cc_start: 0.8535 (mttt) cc_final: 0.8239 (mttt) REVERT: B 954 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.8358 (m170) REVERT: B 969 LYS cc_start: 0.9044 (mttt) cc_final: 0.8772 (mttm) REVERT: B 1017 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8232 (tp30) REVERT: B 1045 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8237 (mmmm) REVERT: B 1084 ASP cc_start: 0.8973 (t0) cc_final: 0.8655 (t0) REVERT: B 1118 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 1119 ASN cc_start: 0.8027 (m-40) cc_final: 0.7626 (m110) REVERT: a 57 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7768 (tt0) REVERT: a 85 SER cc_start: 0.7992 (t) cc_final: 0.7465 (p) REVERT: a 98 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6543 (tpp80) REVERT: a 153 PHE cc_start: 0.8703 (t80) cc_final: 0.7671 (t80) REVERT: a 154 PRO cc_start: 0.8656 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: b 143 PHE cc_start: 0.6737 (p90) cc_final: 0.6421 (p90) REVERT: b 170 GLN cc_start: 0.8211 (tp40) cc_final: 0.7406 (tm-30) REVERT: b 196 TYR cc_start: 0.7206 (m-10) cc_final: 0.6935 (m-10) outliers start: 111 outliers final: 83 residues processed: 683 average time/residue: 0.1995 time to fit residues: 213.8549 Evaluate side-chains 688 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 596 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain a residue 39 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 152 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 216 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.0060 chunk 295 optimal weight: 0.8980 chunk 339 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 914 ASN C 955 ASN C1125 ASN B 762 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN a 5 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 206 HIS ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** 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 = 0.4310 r_free = 0.4310 target = 0.169423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129485 restraints weight = 67191.296| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.99 r_work: 0.3548 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 30500 Z= 0.304 Angle : 0.755 10.122 41519 Z= 0.393 Chirality : 0.050 0.250 4671 Planarity : 0.005 0.061 5342 Dihedral : 5.140 52.867 4092 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.50 % Allowed : 16.48 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: 3749 helix: 0.19 (0.21), residues: 646 sheet: 0.32 (0.16), residues: 921 loop : -1.13 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 567 TYR 0.026 0.002 TYR B 204 PHE 0.045 0.003 PHE B 329 TRP 0.043 0.002 TRP B 104 HIS 0.035 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.30 (30457) covalent geometry : angle 0.75133 / 0.39 (41433) SS BOND : bond 0.00405 / 0.26 ( 43) SS BOND : angle 1.80382 / 1.34 ( 86) hydrogen bonds : bond 0.04818 / 3.24 ( 853) hydrogen bonds : angle 5.52810 / 3.80 ( 2418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 647 time to evaluate : 1.120 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: A 46 SER cc_start: 0.8229 (m) cc_final: 0.7850 (p) REVERT: A 138 ASP cc_start: 0.8453 (t0) cc_final: 0.8199 (t0) REVERT: A 206 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8511 (tptp) REVERT: A 221 SER cc_start: 0.8877 (t) cc_final: 0.8477 (p) REVERT: A 298 GLU cc_start: 0.8810 (tp30) cc_final: 0.8145 (tp30) REVERT: A 314 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 564 GLN cc_start: 0.8754 (tt0) cc_final: 0.8365 (mm110) REVERT: A 606 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8604 (t0) REVERT: A 616 ASN cc_start: 0.7147 (m-40) cc_final: 0.6929 (m-40) REVERT: A 750 SER cc_start: 0.8989 (m) cc_final: 0.8786 (p) REVERT: A 776 LYS cc_start: 0.8603 (mttt) cc_final: 0.8401 (ttmm) REVERT: A 779 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8031 (tm-30) REVERT: A 823 PHE cc_start: 0.8983 (t80) cc_final: 0.8728 (t80) REVERT: A 868 GLU cc_start: 0.8479 (tt0) cc_final: 0.8111 (tm-30) REVERT: A 869 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: A 937 SER cc_start: 0.9053 (m) cc_final: 0.8759 (t) REVERT: A 955 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8477 (t0) REVERT: A 969 LYS cc_start: 0.9175 (mttt) cc_final: 0.8718 (mtpp) REVERT: A 988 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8221 (tp30) REVERT: A 1002 GLN cc_start: 0.8720 (tp40) cc_final: 0.8292 (mm-40) REVERT: A 1017 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8261 (tm-30) REVERT: A 1084 ASP cc_start: 0.8604 (p0) cc_final: 0.8250 (p0) REVERT: C 92 PHE cc_start: 0.8014 (t80) cc_final: 0.7743 (t80) REVERT: C 106 PHE cc_start: 0.7510 (m-80) cc_final: 0.7282 (m-80) REVERT: C 173 GLN cc_start: 0.7335 (pp30) cc_final: 0.7099 (pp30) REVERT: C 189 LEU cc_start: 0.8419 (tp) cc_final: 0.7882 (pp) REVERT: C 220 PHE cc_start: 0.7916 (t80) cc_final: 0.7477 (t80) REVERT: C 237 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7192 (mtm180) REVERT: C 275 PHE cc_start: 0.8113 (m-80) cc_final: 0.7821 (m-80) REVERT: C 290 ASP cc_start: 0.8585 (t0) cc_final: 0.8348 (t70) REVERT: C 304 LYS cc_start: 0.9244 (mttt) cc_final: 0.8929 (mmmm) REVERT: C 347 PHE cc_start: 0.4814 (m-80) cc_final: 0.4412 (m-80) REVERT: C 390 LEU cc_start: 0.8122 (mt) cc_final: 0.7816 (mt) REVERT: C 498 ARG cc_start: 0.6696 (ptt-90) cc_final: 0.5951 (ptt-90) REVERT: C 529 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (tppp) REVERT: C 537 LYS cc_start: 0.9299 (tptt) cc_final: 0.8921 (tptm) REVERT: C 539 VAL cc_start: 0.8740 (m) cc_final: 0.8415 (m) REVERT: C 707 TYR cc_start: 0.4632 (m-80) cc_final: 0.3553 (m-80) REVERT: C 710 ASN cc_start: 0.8473 (m110) cc_final: 0.8204 (p0) REVERT: C 740 MET cc_start: 0.8588 (mmp) cc_final: 0.8221 (mmm) REVERT: C 775 ASP cc_start: 0.8371 (m-30) cc_final: 0.7933 (t0) REVERT: C 814 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8609 (mmmt) REVERT: C 816 SER cc_start: 0.8875 (p) cc_final: 0.8613 (t) REVERT: C 820 ASP cc_start: 0.8946 (t0) cc_final: 0.8557 (m-30) REVERT: C 884 SER cc_start: 0.9044 (m) cc_final: 0.8616 (t) REVERT: C 921 LYS cc_start: 0.9183 (mttt) cc_final: 0.8909 (mttt) REVERT: C 957 GLN cc_start: 0.8656 (tt0) cc_final: 0.8159 (tt0) REVERT: C 1002 GLN cc_start: 0.8575 (tp40) cc_final: 0.7975 (tm-30) REVERT: C 1073 LYS cc_start: 0.8835 (mttt) cc_final: 0.8558 (mttm) REVERT: C 1139 ASP cc_start: 0.8757 (t0) cc_final: 0.8518 (t0) REVERT: c 34 MET cc_start: 0.4750 (mmm) cc_final: 0.3746 (mmm) REVERT: B 79 PHE cc_start: 0.7787 (m-80) cc_final: 0.7453 (m-80) REVERT: B 200 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.4597 (m-80) REVERT: B 206 LYS cc_start: 0.8336 (tppt) cc_final: 0.7886 (tptp) REVERT: B 224 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: B 228 ASP cc_start: 0.7272 (t0) cc_final: 0.6862 (t0) REVERT: B 237 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7278 (mpp80) REVERT: B 276 LEU cc_start: 0.8905 (tp) cc_final: 0.8638 (tt) REVERT: B 304 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8771 (mmtp) REVERT: B 351 TYR cc_start: 0.8449 (p90) cc_final: 0.8213 (p90) REVERT: B 421 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: B 451 TYR cc_start: 0.6407 (m-10) cc_final: 0.5929 (m-10) REVERT: B 495 TYR cc_start: 0.5786 (m-80) cc_final: 0.5362 (m-80) REVERT: B 562 PHE cc_start: 0.7330 (m-10) cc_final: 0.7094 (m-10) REVERT: B 592 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.6152 (p90) REVERT: B 675 GLN cc_start: 0.7349 (mm-40) cc_final: 0.7050 (mm-40) REVERT: B 742 ILE cc_start: 0.9233 (mm) cc_final: 0.9030 (mt) REVERT: B 765 ARG cc_start: 0.8489 (tmm-80) cc_final: 0.7624 (ttp80) REVERT: B 776 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8797 (ttmm) REVERT: B 868 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 884 SER cc_start: 0.9287 (m) cc_final: 0.8889 (t) REVERT: B 1045 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8286 (mmmm) REVERT: B 1084 ASP cc_start: 0.9070 (t0) cc_final: 0.8694 (t0) REVERT: B 1118 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7413 (p0) REVERT: B 1119 ASN cc_start: 0.8104 (m-40) cc_final: 0.7638 (m110) REVERT: a 23 LYS cc_start: 0.8892 (tttp) cc_final: 0.8552 (tptm) REVERT: a 36 TRP cc_start: 0.7715 (m100) cc_final: 0.7237 (m100) REVERT: a 57 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8124 (tt0) REVERT: a 153 PHE cc_start: 0.8774 (t80) cc_final: 0.7732 (t80) REVERT: b 143 PHE cc_start: 0.6849 (p90) cc_final: 0.6522 (p90) REVERT: b 170 GLN cc_start: 0.8279 (tp40) cc_final: 0.7530 (tm-30) outliers start: 116 outliers final: 90 residues processed: 703 average time/residue: 0.2034 time to fit residues: 225.6536 Evaluate side-chains 716 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 616 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 954 HIS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 34 TYR Chi-restraints excluded: chain b residue 41 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 15 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 chunk 329 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 690 GLN A 901 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 564 GLN C1125 ASN B 173 GLN B 321 GLN B 580 GLN B1074 ASN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.173347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.134058 restraints weight = 67299.783| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 4.04 r_work: 0.3607 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.7779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30500 Z= 0.131 Angle : 0.656 11.295 41519 Z= 0.334 Chirality : 0.046 0.278 4671 Planarity : 0.005 0.079 5342 Dihedral : 4.856 52.420 4092 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.59 % Allowed : 18.62 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.52 (0.13), residues: 3749 helix: 0.66 (0.22), residues: 630 sheet: 0.46 (0.17), residues: 889 loop : -1.01 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 567 TYR 0.020 0.001 TYR a 27 PHE 0.030 0.002 PHE C 275 TRP 0.063 0.003 TRP B 436 HIS 0.009 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (30457) covalent geometry : angle 0.65433 / 0.33 (41433) SS BOND : bond 0.00209 / 0.14 ( 43) SS BOND : angle 1.31573 / 0.99 ( 86) hydrogen bonds : bond 0.03782 / 2.55 ( 853) hydrogen bonds : angle 5.28911 / 3.64 ( 2418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 624 time to evaluate : 1.107 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 106 PHE cc_start: 0.6308 (m-10) cc_final: 0.6103 (m-80) REVERT: A 160 TYR cc_start: 0.7221 (p90) cc_final: 0.7014 (p90) REVERT: A 190 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7271 (mtt180) REVERT: A 206 LYS cc_start: 0.8831 (tmtt) cc_final: 0.8277 (tptp) REVERT: A 221 SER cc_start: 0.8766 (t) cc_final: 0.8392 (p) REVERT: A 298 GLU cc_start: 0.8642 (tp30) cc_final: 0.8039 (tt0) REVERT: A 564 GLN cc_start: 0.8734 (tt0) cc_final: 0.8281 (mm110) REVERT: A 606 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8655 (t0) REVERT: A 616 ASN cc_start: 0.7094 (m-40) cc_final: 0.6072 (m-40) REVERT: A 750 SER cc_start: 0.8915 (m) cc_final: 0.8674 (p) REVERT: A 776 LYS cc_start: 0.8528 (mttt) cc_final: 0.8265 (ttmm) REVERT: A 779 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8041 (tm-30) REVERT: A 823 PHE cc_start: 0.8910 (t80) cc_final: 0.8638 (t80) REVERT: A 868 GLU cc_start: 0.8277 (tt0) cc_final: 0.7935 (tm-30) REVERT: A 869 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: A 937 SER cc_start: 0.9006 (m) cc_final: 0.8723 (t) REVERT: A 955 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (t0) REVERT: A 964 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8990 (mmmt) REVERT: A 969 LYS cc_start: 0.9252 (mttt) cc_final: 0.8736 (mtpp) REVERT: A 988 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8136 (tp30) REVERT: A 1002 GLN cc_start: 0.8567 (tp40) cc_final: 0.8167 (mm-40) REVERT: A 1017 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 1084 ASP cc_start: 0.8515 (p0) cc_final: 0.8161 (p0) REVERT: C 106 PHE cc_start: 0.7466 (m-80) cc_final: 0.7194 (m-80) REVERT: C 133 PHE cc_start: 0.7864 (m-80) cc_final: 0.7619 (m-80) REVERT: C 173 GLN cc_start: 0.7437 (pp30) cc_final: 0.6953 (pp30) REVERT: C 237 ARG cc_start: 0.7636 (mtm180) cc_final: 0.7287 (mtm180) REVERT: C 275 PHE cc_start: 0.8035 (m-80) cc_final: 0.7792 (m-80) REVERT: C 304 LYS cc_start: 0.9230 (mttt) cc_final: 0.8902 (mmmm) REVERT: C 331 ASN cc_start: 0.5758 (OUTLIER) cc_final: 0.5494 (p0) REVERT: C 389 ASP cc_start: 0.8849 (m-30) cc_final: 0.8531 (p0) REVERT: C 498 ARG cc_start: 0.6646 (ptt-90) cc_final: 0.5728 (ptt-90) REVERT: C 537 LYS cc_start: 0.9210 (tptt) cc_final: 0.8919 (tptm) REVERT: C 552 LEU cc_start: 0.8376 (mt) cc_final: 0.8174 (mt) REVERT: C 580 GLN cc_start: 0.7870 (tp40) cc_final: 0.7638 (tp40) REVERT: C 710 ASN cc_start: 0.8454 (m110) cc_final: 0.8144 (p0) REVERT: C 775 ASP cc_start: 0.8301 (m-30) cc_final: 0.7968 (t0) REVERT: C 814 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8570 (mmmt) REVERT: C 820 ASP cc_start: 0.8861 (t0) cc_final: 0.8480 (m-30) REVERT: C 884 SER cc_start: 0.8936 (m) cc_final: 0.8495 (t) REVERT: C 979 ASP cc_start: 0.8437 (m-30) cc_final: 0.8209 (m-30) REVERT: C 1002 GLN cc_start: 0.8414 (tp40) cc_final: 0.7831 (tm-30) REVERT: C 1006 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 1073 LYS cc_start: 0.8742 (mttt) cc_final: 0.8424 (mttm) REVERT: C 1139 ASP cc_start: 0.8609 (t0) cc_final: 0.8365 (t0) REVERT: C 1144 GLU cc_start: 0.8240 (pt0) cc_final: 0.8010 (pt0) REVERT: c 34 MET cc_start: 0.4569 (mmm) cc_final: 0.3522 (mmm) REVERT: B 79 PHE cc_start: 0.7909 (m-80) cc_final: 0.7669 (m-80) REVERT: B 191 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7464 (mp0) REVERT: B 202 LYS cc_start: 0.7912 (tptt) cc_final: 0.7374 (tptt) REVERT: B 206 LYS cc_start: 0.8195 (tppt) cc_final: 0.6757 (tptp) REVERT: B 224 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6216 (mp0) REVERT: B 237 ARG cc_start: 0.7558 (mtt-85) cc_final: 0.7106 (mpp80) REVERT: B 276 LEU cc_start: 0.8864 (tp) cc_final: 0.8573 (tt) REVERT: B 351 TYR cc_start: 0.8465 (p90) cc_final: 0.8229 (p90) REVERT: B 355 ARG cc_start: 0.7875 (ttt180) cc_final: 0.7393 (tpp80) REVERT: B 675 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6989 (mm-40) REVERT: B 702 GLU cc_start: 0.8463 (tp30) cc_final: 0.8222 (tp30) REVERT: B 742 ILE cc_start: 0.9260 (mm) cc_final: 0.9013 (mt) REVERT: B 776 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8816 (ttmm) REVERT: B 805 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 868 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 884 SER cc_start: 0.9189 (m) cc_final: 0.8778 (t) REVERT: B 954 HIS cc_start: 0.8610 (m-70) cc_final: 0.8283 (m170) REVERT: B 979 ASP cc_start: 0.8796 (m-30) cc_final: 0.8284 (t0) REVERT: B 984 LEU cc_start: 0.8661 (mt) cc_final: 0.8403 (tp) REVERT: B 1045 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8254 (mmmm) REVERT: B 1084 ASP cc_start: 0.8985 (t0) cc_final: 0.8673 (t0) REVERT: B 1118 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7346 (p0) REVERT: B 1119 ASN cc_start: 0.7996 (m-40) cc_final: 0.7560 (m110) REVERT: a 57 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7978 (tt0) REVERT: a 59 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8076 (ttm-80) REVERT: a 85 SER cc_start: 0.7974 (t) cc_final: 0.7466 (p) REVERT: a 98 ARG cc_start: 0.7056 (mmm160) cc_final: 0.6267 (tpp80) REVERT: a 153 PHE cc_start: 0.8703 (t80) cc_final: 0.7990 (t80) REVERT: b 143 PHE cc_start: 0.6562 (p90) cc_final: 0.6268 (p90) REVERT: b 170 GLN cc_start: 0.8370 (tp40) cc_final: 0.7699 (tm-30) REVERT: b 196 TYR cc_start: 0.7132 (m-10) cc_final: 0.6798 (m-10) outliers start: 86 outliers final: 62 residues processed: 668 average time/residue: 0.1995 time to fit residues: 210.7224 Evaluate side-chains 673 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 602 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain a residue 4 LEU Chi-restraints excluded: chain a residue 39 GLN Chi-restraints excluded: chain a residue 50 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 61 ASN Chi-restraints excluded: chain a residue 199 THR Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 152 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 44 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.0670 chunk 256 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 755 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** a 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.173447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134135 restraints weight = 67790.016| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 4.08 r_work: 0.3602 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.290 30500 Z= 0.252 Angle : 0.827 59.182 41519 Z= 0.470 Chirality : 0.047 0.820 4671 Planarity : 0.005 0.135 5342 Dihedral : 4.861 52.246 4092 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 19.07 % Favored : 78.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.48 % 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: -0.52 (0.13), residues: 3749 helix: 0.66 (0.22), residues: 630 sheet: 0.46 (0.17), residues: 889 loop : -1.00 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 765 TYR 0.050 0.001 TYR A 655 PHE 0.102 0.002 PHE A 643 TRP 0.044 0.003 TRP B 353 HIS 0.004 0.001 HIS a 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (30457) covalent geometry : angle 0.82557 / 0.47 (41433) SS BOND : bond 0.00211 / 0.14 ( 43) SS BOND : angle 1.33798 / 1.01 ( 86) hydrogen bonds : bond 0.03780 / 2.55 ( 853) hydrogen bonds : angle 5.28650 / 3.64 ( 2418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9177.89 seconds wall clock time: 157 minutes 34.61 seconds (9454.61 seconds total)