Starting phenix.real_space_refine on Fri Mar 6 15:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.map" model { file = "/net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wd0_32431/03_2026/7wd0_32431.cif" } resolution = 3.3 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= 0.008 sd= 0.095 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 143 5.16 5 C 20375 2.51 5 N 5310 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 290 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31996 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 8 Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "d" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.09, per 1000 atoms: 0.19 Number of scatterers: 31996 At special positions: 0 Unit cell: (157.392, 159.578, 280.901, 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 143 16.00 O 6168 8.00 N 5310 7.00 C 20375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 199 " distance=2.04 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 94 " distance=2.03 Simple disulfide: pdb=" SG CYS d 139 " - pdb=" SG CYS d 199 " distance=2.03 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7684 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 66 sheets defined 19.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.530A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.794A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.554A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.586A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.560A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.578A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.784A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.987A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.632A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.678A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.908A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.609A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 849 through 854 removed outlier: 3.585A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.650A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.549A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.638A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.808A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.984A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 removed outlier: 3.541A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.561A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.569A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.794A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.316A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.527A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.581A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.526A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.585A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.736A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.517A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.029A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 Processing helix chain 'a' and resid 62 through 65 removed outlier: 3.822A pdb=" N LYS a 65 " --> pdb=" O GLN a 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.879A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 131 removed outlier: 4.348A pdb=" N LEU b 130 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR b 131 " --> pdb=" O SER b 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 126 through 131' Processing helix chain 'b' and resid 188 through 193 removed outlier: 3.535A pdb=" N GLU b 192 " --> pdb=" O LYS b 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 87 through 91 removed outlier: 3.780A pdb=" N SER c 91 " --> pdb=" O PHE c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 160 through 162 No H-bonds generated for 'chain 'c' and resid 160 through 162' Processing helix chain 'd' and resid 129 through 132 Processing helix chain 'd' and resid 188 through 194 removed outlier: 3.659A pdb=" N GLU d 192 " --> pdb=" O LYS d 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS d 194 " --> pdb=" O GLU d 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 188 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.184A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.804A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.200A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 142 removed outlier: 7.635A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.525A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.815A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.844A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.618A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.969A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.562A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.791A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.886A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.493A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.601A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.000A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 140 through 142 removed outlier: 4.146A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.563A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.636A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.095A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.382A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.166A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.646A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.955A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.813A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.487A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 357 through 361 removed outlier: 3.672A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 393 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.014A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.674A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'a' and resid 3 through 6 removed outlier: 3.574A pdb=" N GLN a 3 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL a 18 " --> pdb=" O PHE a 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU a 82 " --> pdb=" O THR a 69 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR a 69 " --> pdb=" O GLU a 82 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR a 33 " --> pdb=" O ASP a 99 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP a 57 " --> pdb=" O ASN a 52 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.759A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.742A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 10 through 12 removed outlier: 6.889A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU b 39 " --> pdb=" O TYR b 55 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR b 55 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.637A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 122 through 123 removed outlier: 3.924A pdb=" N PHE b 123 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL b 138 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.872A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'c' and resid 3 through 6 removed outlier: 3.505A pdb=" N GLN c 3 " --> pdb=" O SER c 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL c 18 " --> pdb=" O PHE c 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR c 78 " --> pdb=" O ASP c 73 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR c 71 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU c 82 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR c 69 " --> pdb=" O GLU c 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 10 through 12 removed outlier: 3.993A pdb=" N THR c 114 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL c 12 " --> pdb=" O THR c 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL c 113 " --> pdb=" O ALA c 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA c 92 " --> pdb=" O VAL c 113 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR c 33 " --> pdb=" O ASP c 99 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N MET c 34 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP c 36 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR c 59 " --> pdb=" O GLY c 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 10 through 12 removed outlier: 3.993A pdb=" N THR c 114 " --> pdb=" O GLU c 10 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL c 12 " --> pdb=" O THR c 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL c 113 " --> pdb=" O ALA c 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA c 92 " --> pdb=" O VAL c 113 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 124 through 128 removed outlier: 4.482A pdb=" N GLY c 143 " --> pdb=" O LEU c 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS c 144 " --> pdb=" O SER c 183 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER c 183 " --> pdb=" O CYS c 144 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 157 through 158 removed outlier: 4.015A pdb=" N VAL c 197 " --> pdb=" O ILE c 214 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 173 through 175 Processing sheet with id=AG9, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.611A pdb=" N THR d 22 " --> pdb=" O SER d 7 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL d 19 " --> pdb=" O ILE d 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE d 77 " --> pdb=" O CYS d 23 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP d 76 " --> pdb=" O SER d 73 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'd' and resid 10 through 12 removed outlier: 6.900A pdb=" N LEU d 11 " --> pdb=" O GLU d 111 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU d 39 " --> pdb=" O TYR d 55 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TYR d 55 " --> pdb=" O LEU d 39 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TRP d 41 " --> pdb=" O LEU d 53 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 122 through 123 removed outlier: 3.976A pdb=" N PHE d 123 " --> pdb=" O VAL d 138 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL d 138 " --> pdb=" O PHE d 123 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR d 178 " --> pdb=" O ASN d 143 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 158 through 159 removed outlier: 3.840A pdb=" N ASN d 150 " --> pdb=" O THR d 202 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS d 212 " --> pdb=" O CYS d 199 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA d 201 " --> pdb=" O ILE d 210 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3039 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: 7.96 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10275 1.35 - 1.48: 8542 1.48 - 1.61: 13749 1.61 - 1.73: 0 1.73 - 1.86: 183 Bond restraints: 32749 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.06e-02 8.90e+03 1.89e+01 bond pdb=" C GLN B1142 " pdb=" N PRO B1143 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.06e-02 8.90e+03 1.58e+01 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.337 1.378 -0.042 1.06e-02 8.90e+03 1.55e+01 bond pdb=" C GLY B 526 " pdb=" N PRO B 527 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" N ALA b 114 " pdb=" CA ALA b 114 " ideal model delta sigma weight residual 1.458 1.529 -0.071 1.90e-02 2.77e+03 1.41e+01 ... (remaining 32744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 44410 3.74 - 7.48: 138 7.48 - 11.22: 8 11.22 - 14.96: 4 14.96 - 18.70: 1 Bond angle restraints: 44561 Sorted by residual: angle pdb=" N VAL C 362 " pdb=" CA VAL C 362 " pdb=" C VAL C 362 " ideal model delta sigma weight residual 109.34 123.85 -14.51 2.08e+00 2.31e-01 4.86e+01 angle pdb=" C LEU B 492 " pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 121.70 133.94 -12.24 1.80e+00 3.09e-01 4.62e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 120.82 129.98 -9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 120.54 128.39 -7.85 1.35e+00 5.49e-01 3.38e+01 angle pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 121.97 132.40 -10.43 1.80e+00 3.09e-01 3.36e+01 ... (remaining 44556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.28: 18735 26.28 - 52.56: 678 52.56 - 78.83: 65 78.83 - 105.11: 19 105.11 - 131.39: 1 Dihedral angle restraints: 19498 sinusoidal: 7552 harmonic: 11946 Sorted by residual: dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 48.61 131.39 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 0.15 -86.15 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.47 -85.53 1 1.00e+01 1.00e-02 8.85e+01 ... (remaining 19495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4277 0.065 - 0.130: 704 0.130 - 0.195: 43 0.195 - 0.260: 6 0.260 - 0.325: 1 Chirality restraints: 5031 Sorted by residual: chirality pdb=" CB ILE b 155 " pdb=" CA ILE b 155 " pdb=" CG1 ILE b 155 " pdb=" CG2 ILE b 155 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ALA d 114 " pdb=" N ALA d 114 " pdb=" C ALA d 114 " pdb=" CB ALA d 114 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR b 119 " pdb=" CA THR b 119 " pdb=" OG1 THR b 119 " pdb=" CG2 THR b 119 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 5028 not shown) Planarity restraints: 5754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 526 " 0.041 2.00e-02 2.50e+03 7.96e-02 6.33e+01 pdb=" C GLY B 526 " -0.138 2.00e-02 2.50e+03 pdb=" O GLY B 526 " 0.054 2.00e-02 2.50e+03 pdb=" N PRO B 527 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 117 " 0.032 2.00e-02 2.50e+03 6.36e-02 4.04e+01 pdb=" C ALA a 117 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA a 117 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA a 118 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 335 " 0.032 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C LEU B 335 " -0.110 2.00e-02 2.50e+03 pdb=" O LEU B 335 " 0.042 2.00e-02 2.50e+03 pdb=" N CYS B 336 " 0.035 2.00e-02 2.50e+03 ... (remaining 5751 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9082 2.81 - 3.33: 24482 3.33 - 3.85: 52139 3.85 - 4.38: 57879 4.38 - 4.90: 102252 Nonbonded interactions: 245834 Sorted by model distance: nonbonded pdb=" OG SER d 121 " pdb=" O PHE d 140 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLU d 111 " pdb=" OH TYR d 178 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR a 149 " pdb=" OE2 GLU a 152 " model vdw 2.305 3.040 nonbonded pdb=" OG SER b 121 " pdb=" O PHE b 140 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.317 3.040 ... (remaining 245829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'b' selection = chain 'd' } 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: 4.120 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.600 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 32791 Z= 0.173 Angle : 0.690 18.702 44645 Z= 0.409 Chirality : 0.046 0.325 5031 Planarity : 0.006 0.080 5754 Dihedral : 12.949 131.391 11688 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.11), residues: 4048 helix: -4.65 (0.05), residues: 665 sheet: -0.25 (0.16), residues: 985 loop : -2.12 (0.10), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.017 0.001 TYR A 380 PHE 0.014 0.001 PHE C 238 TRP 0.012 0.001 TRP d 56 HIS 0.002 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00304 (32749) covalent geometry : angle 0.68751 (44561) SS BOND : bond 0.00570 ( 42) SS BOND : angle 1.62570 ( 84) hydrogen bonds : bond 0.30169 ( 1087) hydrogen bonds : angle 10.44663 ( 3039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 550 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.7616 (t80) cc_final: 0.7350 (t80) REVERT: A 1019 ARG cc_start: 0.7659 (tpt170) cc_final: 0.7374 (tpt170) REVERT: B 77 LYS cc_start: 0.2882 (mmtp) cc_final: 0.1918 (tmtt) REVERT: C 174 PRO cc_start: 0.4887 (Cg_exo) cc_final: 0.4327 (Cg_endo) REVERT: C 759 PHE cc_start: 0.7441 (t80) cc_final: 0.6914 (t80) REVERT: C 979 ASP cc_start: 0.8048 (t70) cc_final: 0.7465 (t70) REVERT: a 55 ILE cc_start: 0.2438 (pt) cc_final: 0.2205 (tt) REVERT: b 189 ASP cc_start: 0.3979 (p0) cc_final: 0.2818 (m-30) REVERT: c 34 MET cc_start: 0.2946 (tpp) cc_final: 0.0252 (pmm) REVERT: d 180 MET cc_start: -0.1396 (ttt) cc_final: -0.1738 (ttt) outliers start: 6 outliers final: 2 residues processed: 556 average time/residue: 0.2235 time to fit residues: 189.8206 Evaluate side-chains 262 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 166 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 149 ASN A 173 GLN A 613 GLN A 703 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 913 GLN A1048 HIS A1119 ASN B 188 ASN B 474 GLN B 563 GLN B 564 GLN B 703 ASN B 710 ASN B 787 GLN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1010 GLN B1011 GLN B1119 ASN C 188 ASN C 334 ASN C 414 GLN C 540 ASN C 644 GLN C 804 GLN C 901 GLN C 914 ASN C1002 GLN C1010 GLN C1048 HIS C1106 GLN b 171 GLN c 39 GLN c 41 HIS c 52 ASN d 44 GLN d 171 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.137750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.110060 restraints weight = 121651.615| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 4.55 r_work: 0.3791 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32791 Z= 0.134 Angle : 0.575 11.545 44645 Z= 0.307 Chirality : 0.044 0.238 5031 Planarity : 0.005 0.065 5754 Dihedral : 4.271 56.162 4391 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.56 % Allowed : 9.92 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.12), residues: 4048 helix: -1.15 (0.16), residues: 700 sheet: -0.00 (0.15), residues: 1062 loop : -1.56 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 454 TYR 0.019 0.001 TYR a 60 PHE 0.029 0.001 PHE B 32 TRP 0.019 0.002 TRP C 152 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00291 (32749) covalent geometry : angle 0.56753 (44561) SS BOND : bond 0.00500 ( 42) SS BOND : angle 2.20730 ( 84) hydrogen bonds : bond 0.05516 ( 1087) hydrogen bonds : angle 6.42020 ( 3039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 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: A 117 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 200 TYR cc_start: 0.8025 (m-80) cc_final: 0.7632 (m-80) REVERT: A 430 THR cc_start: 0.5176 (OUTLIER) cc_final: 0.4952 (t) REVERT: A 878 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9177 (tt) REVERT: A 904 TYR cc_start: 0.7192 (t80) cc_final: 0.6921 (t80) REVERT: A 1019 ARG cc_start: 0.8612 (tpt170) cc_final: 0.8174 (tpt170) REVERT: B 77 LYS cc_start: 0.3019 (mmtp) cc_final: 0.1777 (tmtt) REVERT: B 166 CYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4678 (m) REVERT: B 786 LYS cc_start: 0.8295 (ptmm) cc_final: 0.8032 (tptp) REVERT: B 902 MET cc_start: 0.8916 (mmm) cc_final: 0.8652 (mmt) REVERT: B 904 TYR cc_start: 0.7498 (t80) cc_final: 0.7200 (t80) REVERT: C 238 PHE cc_start: 0.7549 (p90) cc_final: 0.7025 (p90) REVERT: a 203 HIS cc_start: 0.0308 (t-170) cc_final: 0.0069 (t70) REVERT: c 34 MET cc_start: 0.2743 (tpp) cc_final: 0.1308 (mmt) REVERT: c 47 TRP cc_start: 0.3523 (t60) cc_final: 0.2769 (t60) outliers start: 56 outliers final: 19 residues processed: 309 average time/residue: 0.2051 time to fit residues: 100.9409 Evaluate side-chains 222 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 164 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 173 GLN A 360 ASN A 655 HIS A 690 GLN A 703 ASN A 856 ASN B 564 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1048 HIS C 762 GLN b 37 ASN b 95 GLN b 129 GLN c 41 HIS d 44 GLN d 142 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.132024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.104135 restraints weight = 120099.517| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.68 r_work: 0.3697 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32791 Z= 0.217 Angle : 0.649 12.600 44645 Z= 0.346 Chirality : 0.046 0.186 5031 Planarity : 0.005 0.050 5754 Dihedral : 4.735 43.532 4391 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.53 % Allowed : 13.12 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4048 helix: 0.47 (0.19), residues: 711 sheet: -0.07 (0.15), residues: 1055 loop : -1.35 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 44 TYR 0.033 0.002 TYR A 904 PHE 0.019 0.002 PHE B 32 TRP 0.060 0.003 TRP A 886 HIS 0.011 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00490 (32749) covalent geometry : angle 0.64427 (44561) SS BOND : bond 0.00536 ( 42) SS BOND : angle 1.91697 ( 84) hydrogen bonds : bond 0.05057 ( 1087) hydrogen bonds : angle 5.82944 ( 3039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 199 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8059 (mt) REVERT: A 200 TYR cc_start: 0.8014 (m-80) cc_final: 0.7674 (m-80) REVERT: A 451 TYR cc_start: 0.3365 (m-80) cc_final: 0.2868 (t80) REVERT: A 455 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5314 (mm) REVERT: A 979 ASP cc_start: 0.8923 (t0) cc_final: 0.8491 (t0) REVERT: A 1019 ARG cc_start: 0.8659 (tpt170) cc_final: 0.8133 (tpt170) REVERT: B 98 SER cc_start: 0.4731 (p) cc_final: 0.4358 (t) REVERT: B 141 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5359 (pp) REVERT: B 773 GLU cc_start: 0.8822 (tt0) cc_final: 0.8525 (tt0) REVERT: B 786 LYS cc_start: 0.8378 (ptmm) cc_final: 0.8090 (tptp) REVERT: C 353 TRP cc_start: -0.1617 (p90) cc_final: -0.2050 (p90) REVERT: a 81 MET cc_start: -0.2951 (tpp) cc_final: -0.3331 (tpp) REVERT: a 83 PHE cc_start: -0.0425 (OUTLIER) cc_final: -0.1714 (m-80) REVERT: a 185 VAL cc_start: 0.3489 (OUTLIER) cc_final: 0.3174 (m) REVERT: a 203 HIS cc_start: 0.0077 (t-170) cc_final: -0.0304 (t70) REVERT: c 34 MET cc_start: 0.1862 (tpp) cc_final: 0.1110 (tpp) REVERT: c 36 TRP cc_start: 0.1906 (m100) cc_final: 0.1566 (m100) REVERT: c 47 TRP cc_start: 0.3925 (t60) cc_final: 0.1842 (t60) outliers start: 91 outliers final: 50 residues processed: 273 average time/residue: 0.1756 time to fit residues: 81.2270 Evaluate side-chains 219 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 95 TYR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 39 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 359 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 363 optimal weight: 0.0970 chunk 399 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 173 GLN A 703 ASN A 913 GLN B 703 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 245 HIS C 563 GLN C1010 GLN a 41 HIS b 95 GLN c 41 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.131154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102939 restraints weight = 119000.486| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 4.04 r_work: 0.3693 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32791 Z= 0.170 Angle : 0.572 11.355 44645 Z= 0.302 Chirality : 0.044 0.179 5031 Planarity : 0.004 0.062 5754 Dihedral : 4.584 43.830 4389 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.67 % Allowed : 14.68 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.71 (0.13), residues: 4048 helix: 1.23 (0.20), residues: 716 sheet: -0.08 (0.15), residues: 1082 loop : -1.26 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 98 TYR 0.020 0.002 TYR A 451 PHE 0.022 0.002 PHE B 643 TRP 0.033 0.002 TRP A 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00387 (32749) covalent geometry : angle 0.56504 (44561) SS BOND : bond 0.00721 ( 42) SS BOND : angle 2.06186 ( 84) hydrogen bonds : bond 0.04283 ( 1087) hydrogen bonds : angle 5.57056 ( 3039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 186 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7674 (m-80) cc_final: 0.7344 (m-80) REVERT: A 301 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7615 (m) REVERT: A 455 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5850 (mm) REVERT: A 759 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7884 (t80) REVERT: A 904 TYR cc_start: 0.7577 (t80) cc_final: 0.7364 (t80) REVERT: A 979 ASP cc_start: 0.8881 (t0) cc_final: 0.8636 (t0) REVERT: A 1019 ARG cc_start: 0.8714 (tpt170) cc_final: 0.8166 (tpt170) REVERT: B 152 TRP cc_start: 0.1177 (m100) cc_final: 0.0969 (m100) REVERT: B 421 TYR cc_start: 0.3991 (OUTLIER) cc_final: 0.3516 (m-80) REVERT: B 773 GLU cc_start: 0.8702 (tt0) cc_final: 0.8408 (tt0) REVERT: B 955 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8212 (t0) REVERT: C 353 TRP cc_start: -0.1397 (p90) cc_final: -0.2136 (p90) REVERT: a 185 VAL cc_start: 0.3652 (OUTLIER) cc_final: 0.3336 (m) REVERT: b 170 ASP cc_start: 0.2536 (p0) cc_final: 0.1644 (t0) outliers start: 96 outliers final: 50 residues processed: 260 average time/residue: 0.1816 time to fit residues: 79.2141 Evaluate side-chains 222 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 331 ASN A 703 ASN A 710 ASN B 907 ASN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 762 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.130927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.102960 restraints weight = 119552.575| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.85 r_work: 0.3703 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32791 Z= 0.138 Angle : 0.538 10.754 44645 Z= 0.283 Chirality : 0.043 0.166 5031 Planarity : 0.004 0.051 5754 Dihedral : 4.390 43.591 4389 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.67 % Allowed : 15.99 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4048 helix: 1.64 (0.20), residues: 715 sheet: 0.02 (0.15), residues: 1087 loop : -1.19 (0.12), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 98 TYR 0.020 0.001 TYR d 55 PHE 0.014 0.001 PHE B 643 TRP 0.025 0.002 TRP A 886 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00310 (32749) covalent geometry : angle 0.53375 (44561) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.59745 ( 84) hydrogen bonds : bond 0.03893 ( 1087) hydrogen bonds : angle 5.38976 ( 3039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 183 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7887 (m-80) cc_final: 0.7507 (m-80) REVERT: A 301 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7659 (m) REVERT: A 455 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6033 (tp) REVERT: A 979 ASP cc_start: 0.8848 (t0) cc_final: 0.8601 (t0) REVERT: A 1019 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8081 (tpt170) REVERT: B 421 TYR cc_start: 0.3917 (OUTLIER) cc_final: 0.3595 (m-80) REVERT: B 731 MET cc_start: 0.8858 (ttp) cc_final: 0.8606 (ttp) REVERT: B 773 GLU cc_start: 0.8665 (tt0) cc_final: 0.8322 (tt0) REVERT: B 902 MET cc_start: 0.8883 (mmt) cc_final: 0.8492 (mmt) REVERT: C 353 TRP cc_start: -0.1488 (p90) cc_final: -0.2134 (p90) REVERT: a 185 VAL cc_start: 0.3942 (OUTLIER) cc_final: 0.3709 (m) REVERT: b 170 ASP cc_start: 0.2790 (p0) cc_final: 0.1844 (t0) REVERT: c 82 GLU cc_start: 0.0914 (OUTLIER) cc_final: 0.0352 (tp30) outliers start: 96 outliers final: 58 residues processed: 259 average time/residue: 0.1802 time to fit residues: 78.6868 Evaluate side-chains 229 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 338 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 400 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 703 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 762 GLN C1083 HIS ** C1159 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 = 0.4362 r_free = 0.4362 target = 0.130654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.102734 restraints weight = 118919.275| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.88 r_work: 0.3699 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32791 Z= 0.131 Angle : 0.529 11.994 44645 Z= 0.277 Chirality : 0.043 0.167 5031 Planarity : 0.004 0.049 5754 Dihedral : 4.370 43.469 4389 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.59 % Allowed : 16.49 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.38 (0.13), residues: 4048 helix: 1.80 (0.20), residues: 722 sheet: 0.03 (0.15), residues: 1107 loop : -1.12 (0.13), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 98 TYR 0.019 0.001 TYR d 55 PHE 0.040 0.001 PHE B 855 TRP 0.036 0.002 TRP C 886 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00297 (32749) covalent geometry : angle 0.52332 (44561) SS BOND : bond 0.00407 ( 42) SS BOND : angle 1.80603 ( 84) hydrogen bonds : bond 0.03757 ( 1087) hydrogen bonds : angle 5.25907 ( 3039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 173 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.4991 (tpp-160) REVERT: A 301 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7666 (m) REVERT: A 455 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6165 (tp) REVERT: A 759 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.8008 (t80) REVERT: A 878 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9151 (tt) REVERT: A 979 ASP cc_start: 0.8922 (t0) cc_final: 0.8686 (t0) REVERT: A 1019 ARG cc_start: 0.8737 (tpt170) cc_final: 0.8189 (tpt170) REVERT: B 150 LYS cc_start: 0.5558 (OUTLIER) cc_final: 0.5346 (pttt) REVERT: B 421 TYR cc_start: 0.3927 (OUTLIER) cc_final: 0.3447 (m-80) REVERT: B 731 MET cc_start: 0.8756 (ttp) cc_final: 0.8496 (ttp) REVERT: B 773 GLU cc_start: 0.8656 (tt0) cc_final: 0.8312 (tt0) REVERT: C 153 MET cc_start: 0.3485 (pmm) cc_final: 0.3184 (pmm) REVERT: C 353 TRP cc_start: -0.1479 (p90) cc_final: -0.2167 (p90) REVERT: c 82 GLU cc_start: 0.0545 (OUTLIER) cc_final: -0.0170 (tp30) outliers start: 93 outliers final: 67 residues processed: 251 average time/residue: 0.1807 time to fit residues: 76.4771 Evaluate side-chains 237 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 155 THR Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 337 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 402 optimal weight: 0.9990 chunk 332 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 703 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 185 ASN B 703 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.128500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.102099 restraints weight = 119800.546| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.83 r_work: 0.3649 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32791 Z= 0.187 Angle : 0.609 12.447 44645 Z= 0.320 Chirality : 0.045 0.172 5031 Planarity : 0.004 0.055 5754 Dihedral : 4.797 44.914 4389 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.06 % Allowed : 16.99 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4048 helix: 1.77 (0.20), residues: 713 sheet: -0.05 (0.15), residues: 1087 loop : -1.30 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 98 TYR 0.021 0.002 TYR d 55 PHE 0.027 0.002 PHE C 855 TRP 0.071 0.002 TRP C 886 HIS 0.006 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00427 (32749) covalent geometry : angle 0.60469 (44561) SS BOND : bond 0.00520 ( 42) SS BOND : angle 1.73291 ( 84) hydrogen bonds : bond 0.04311 ( 1087) hydrogen bonds : angle 5.55415 ( 3039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 176 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7597 (m) REVERT: A 455 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6166 (tp) REVERT: A 878 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9217 (tt) REVERT: A 979 ASP cc_start: 0.8987 (t0) cc_final: 0.8739 (t0) REVERT: A 1019 ARG cc_start: 0.8763 (tpt170) cc_final: 0.8194 (tpt170) REVERT: B 150 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.5027 (pttt) REVERT: B 177 MET cc_start: -0.1639 (mmp) cc_final: -0.1928 (mmp) REVERT: B 323 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8367 (t) REVERT: B 421 TYR cc_start: 0.4416 (OUTLIER) cc_final: 0.3966 (m-80) REVERT: B 759 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 773 GLU cc_start: 0.8673 (tt0) cc_final: 0.8332 (tt0) REVERT: C 353 TRP cc_start: -0.1151 (p90) cc_final: -0.1862 (p90) REVERT: C 759 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7796 (t80) REVERT: C 1005 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8403 (mm-40) REVERT: a 34 MET cc_start: 0.3453 (tpt) cc_final: 0.0364 (ptm) REVERT: a 51 ILE cc_start: 0.3551 (tt) cc_final: 0.2581 (tt) REVERT: a 81 MET cc_start: -0.3137 (tpp) cc_final: -0.3399 (tpp) REVERT: b 4 MET cc_start: 0.0695 (tmm) cc_final: -0.0467 (ptm) REVERT: b 166 ASN cc_start: 0.3488 (m-40) cc_final: 0.3032 (t0) REVERT: c 82 GLU cc_start: 0.0385 (OUTLIER) cc_final: 0.0056 (tp30) outliers start: 110 outliers final: 72 residues processed: 263 average time/residue: 0.1719 time to fit residues: 77.2163 Evaluate side-chains 246 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain a residue 2 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 71 THR Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 112 optimal weight: 0.7980 chunk 378 optimal weight: 4.9990 chunk 267 optimal weight: 0.0970 chunk 256 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 chunk 324 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN C 437 ASN C 762 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 HIS d 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.129466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.102982 restraints weight = 120292.065| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.51 r_work: 0.3681 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 32791 Z= 0.130 Angle : 0.543 11.877 44645 Z= 0.283 Chirality : 0.043 0.179 5031 Planarity : 0.004 0.058 5754 Dihedral : 4.505 43.109 4389 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.53 % Allowed : 17.83 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 4048 helix: 1.95 (0.20), residues: 716 sheet: 0.00 (0.15), residues: 1081 loop : -1.22 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.034 0.001 TYR C 904 PHE 0.031 0.001 PHE B 855 TRP 0.076 0.002 TRP C 886 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00299 (32749) covalent geometry : angle 0.53992 (44561) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.47765 ( 84) hydrogen bonds : bond 0.03760 ( 1087) hydrogen bonds : angle 5.34568 ( 3039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 173 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 CYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7549 (m) REVERT: A 455 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6265 (tp) REVERT: A 878 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9226 (tt) REVERT: A 979 ASP cc_start: 0.8933 (t0) cc_final: 0.8700 (t0) REVERT: A 1019 ARG cc_start: 0.8771 (tpt170) cc_final: 0.8196 (tpt170) REVERT: B 141 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5845 (pp) REVERT: B 177 MET cc_start: -0.1779 (mmp) cc_final: -0.2105 (mmp) REVERT: B 323 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8374 (t) REVERT: B 421 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.4012 (m-80) REVERT: B 759 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7730 (t80) REVERT: B 773 GLU cc_start: 0.8652 (tt0) cc_final: 0.8294 (tt0) REVERT: B 902 MET cc_start: 0.8893 (mmt) cc_final: 0.8596 (mmt) REVERT: C 353 TRP cc_start: -0.1229 (p90) cc_final: -0.1921 (p90) REVERT: a 10 GLU cc_start: 0.1205 (mp0) cc_final: -0.0766 (tt0) REVERT: a 94 TYR cc_start: 0.2361 (OUTLIER) cc_final: 0.2054 (t80) REVERT: b 4 MET cc_start: -0.0034 (tmm) cc_final: -0.1385 (ptm) REVERT: c 82 GLU cc_start: 0.0664 (OUTLIER) cc_final: 0.0109 (tp30) outliers start: 91 outliers final: 66 residues processed: 247 average time/residue: 0.1755 time to fit residues: 74.1515 Evaluate side-chains 235 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 94 TYR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 328 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 129 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 333 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 399 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.129994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102894 restraints weight = 118250.214| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.42 r_work: 0.3691 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32791 Z= 0.112 Angle : 0.526 11.740 44645 Z= 0.274 Chirality : 0.043 0.153 5031 Planarity : 0.004 0.047 5754 Dihedral : 4.374 42.293 4389 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.53 % Allowed : 17.60 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4048 helix: 2.06 (0.20), residues: 720 sheet: 0.10 (0.15), residues: 1079 loop : -1.19 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 102 TYR 0.020 0.001 TYR d 55 PHE 0.023 0.001 PHE a 170 TRP 0.066 0.002 TRP C 886 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00255 (32749) covalent geometry : angle 0.51948 (44561) SS BOND : bond 0.00351 ( 42) SS BOND : angle 2.02632 ( 84) hydrogen bonds : bond 0.03517 ( 1087) hydrogen bonds : angle 5.17534 ( 3039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 176 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8002 (mm) cc_final: 0.7759 (mm) REVERT: A 301 CYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7546 (m) REVERT: A 455 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6412 (tp) REVERT: A 878 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9217 (tt) REVERT: A 979 ASP cc_start: 0.8908 (t0) cc_final: 0.8688 (t0) REVERT: A 1019 ARG cc_start: 0.8709 (tpt170) cc_final: 0.8125 (tpt170) REVERT: B 141 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.6062 (pp) REVERT: B 177 MET cc_start: -0.1824 (mmp) cc_final: -0.2151 (mmp) REVERT: B 323 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 421 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.3922 (m-80) REVERT: B 759 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 773 GLU cc_start: 0.8611 (tt0) cc_final: 0.8275 (tt0) REVERT: B 902 MET cc_start: 0.8893 (mmt) cc_final: 0.8576 (mmt) REVERT: B 1002 GLN cc_start: 0.8677 (tt0) cc_final: 0.8272 (tm-30) REVERT: C 353 TRP cc_start: -0.1270 (p90) cc_final: -0.1941 (p90) REVERT: C 759 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7873 (t80) REVERT: a 10 GLU cc_start: 0.1287 (mp0) cc_final: -0.0941 (tt0) REVERT: a 94 TYR cc_start: 0.2061 (OUTLIER) cc_final: 0.1706 (t80) REVERT: b 4 MET cc_start: 0.0133 (tmm) cc_final: -0.1176 (ptm) REVERT: c 36 TRP cc_start: 0.2466 (m100) cc_final: 0.2220 (m100) REVERT: c 82 GLU cc_start: 0.1168 (OUTLIER) cc_final: 0.0637 (tp30) REVERT: c 199 CYS cc_start: -0.2498 (OUTLIER) cc_final: -0.3147 (p) outliers start: 91 outliers final: 67 residues processed: 251 average time/residue: 0.1732 time to fit residues: 74.4460 Evaluate side-chains 247 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 169 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 94 TYR Chi-restraints excluded: chain a residue 109 GLN Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 199 CYS Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 182 optimal weight: 3.9990 chunk 369 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 330 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 914 ASN C 762 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 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 = 0.4318 r_free = 0.4318 target = 0.127758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.100358 restraints weight = 118865.379| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.86 r_work: 0.3666 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32791 Z= 0.197 Angle : 0.619 12.249 44645 Z= 0.323 Chirality : 0.045 0.168 5031 Planarity : 0.004 0.055 5754 Dihedral : 4.731 42.138 4389 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.45 % Allowed : 17.97 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4048 helix: 1.83 (0.20), residues: 732 sheet: -0.08 (0.15), residues: 1099 loop : -1.34 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 98 TYR 0.022 0.002 TYR b 92 PHE 0.049 0.002 PHE C 855 TRP 0.078 0.002 TRP C 886 HIS 0.007 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00451 (32749) covalent geometry : angle 0.61260 (44561) SS BOND : bond 0.00475 ( 42) SS BOND : angle 2.08721 ( 84) hydrogen bonds : bond 0.04176 ( 1087) hydrogen bonds : angle 5.44501 ( 3039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 CYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7393 (m) REVERT: A 979 ASP cc_start: 0.8944 (t0) cc_final: 0.8735 (t0) REVERT: A 1019 ARG cc_start: 0.8732 (tpt170) cc_final: 0.8137 (tpt170) REVERT: B 141 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6117 (pp) REVERT: B 177 MET cc_start: -0.1753 (mmp) cc_final: -0.1991 (mmt) REVERT: B 323 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (t) REVERT: B 421 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3486 (m-80) REVERT: B 444 LYS cc_start: 0.2235 (pttm) cc_final: 0.1896 (ttpt) REVERT: B 759 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7578 (t80) REVERT: B 773 GLU cc_start: 0.8678 (tt0) cc_final: 0.8334 (tt0) REVERT: C 221 SER cc_start: 0.9006 (t) cc_final: 0.8720 (p) REVERT: C 353 TRP cc_start: -0.1177 (p90) cc_final: -0.1917 (p90) REVERT: C 759 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.7883 (t80) REVERT: a 34 MET cc_start: 0.3586 (tpt) cc_final: 0.0424 (ptm) REVERT: a 94 TYR cc_start: 0.2153 (OUTLIER) cc_final: 0.1648 (t80) REVERT: b 4 MET cc_start: -0.0171 (tmm) cc_final: -0.1730 (ptm) REVERT: b 104 PHE cc_start: 0.3684 (OUTLIER) cc_final: 0.2812 (t80) REVERT: b 166 ASN cc_start: 0.3364 (m-40) cc_final: 0.2994 (t0) REVERT: c 19 LYS cc_start: 0.3665 (mttt) cc_final: 0.2822 (ptmt) REVERT: c 82 GLU cc_start: 0.0376 (OUTLIER) cc_final: -0.0205 (tp30) REVERT: c 101 LYS cc_start: 0.3463 (mtpt) cc_final: 0.3154 (mmtt) REVERT: c 199 CYS cc_start: -0.2849 (OUTLIER) cc_final: -0.3320 (p) outliers start: 88 outliers final: 74 residues processed: 242 average time/residue: 0.1767 time to fit residues: 73.1097 Evaluate side-chains 246 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 162 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 94 TYR Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 169 THR Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain b residue 104 PHE Chi-restraints excluded: chain b residue 130 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain c residue 82 GLU Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 199 CYS Chi-restraints excluded: chain d residue 13 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 20 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 304 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 384 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 762 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 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 = 0.4344 r_free = 0.4344 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.103121 restraints weight = 118701.633| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.64 r_work: 0.3693 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32791 Z= 0.112 Angle : 0.534 11.519 44645 Z= 0.277 Chirality : 0.043 0.149 5031 Planarity : 0.004 0.046 5754 Dihedral : 4.428 39.073 4389 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.28 % Allowed : 18.30 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4048 helix: 2.19 (0.20), residues: 713 sheet: 0.01 (0.15), residues: 1110 loop : -1.28 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.020 0.001 TYR d 55 PHE 0.043 0.001 PHE C 855 TRP 0.053 0.002 TRP C 886 HIS 0.004 0.001 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.00252 (32749) covalent geometry : angle 0.53000 (44561) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.55427 ( 84) hydrogen bonds : bond 0.03544 ( 1087) hydrogen bonds : angle 5.23939 ( 3039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9870.85 seconds wall clock time: 168 minutes 59.29 seconds (10139.29 seconds total)