Starting phenix.real_space_refine on Fri Jun 27 19:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wd0_32431/06_2025/7wd0_32431.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wd0_32431/06_2025/7wd0_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_32431/06_2025/7wd0_32431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wd0_32431/06_2025/7wd0_32431.map" model { file = "/net/cci-nas-00/data/ceres_data/7wd0_32431/06_2025/7wd0_32431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wd0_32431/06_2025/7wd0_32431.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.50s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.72, per 1000 atoms: 0.59 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: 7.07 Conformation dependent library (CDL) restraints added in 4.2 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: 4.80 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: 15.34 Time building geometry restraints manager: 8.49 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: 0.02 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 72.680 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.640 ------------------------------------------------------------------------------- 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 : 2.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP d 56 HIS 0.002 0.000 HIS C 146 PHE 0.014 0.001 PHE C 238 TYR 0.017 0.001 TYR A 380 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.30169 ( 1087) hydrogen bonds : angle 10.44663 ( 3039) SS BOND : bond 0.00570 ( 42) SS BOND : angle 1.62570 ( 84) covalent geometry : bond 0.00304 (32749) covalent geometry : angle 0.68751 (44561) *********************** 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 : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.7616 (t80) cc_final: 0.7350 (t80) REVERT: A 1019 ARG cc_start: 0.7659 (tpt170) cc_final: 0.7375 (tpt170) REVERT: C 174 PRO cc_start: 0.4887 (Cg_exo) cc_final: 0.4326 (Cg_endo) REVERT: C 979 ASP cc_start: 0.8048 (t70) cc_final: 0.7464 (t70) REVERT: a 55 ILE cc_start: 0.2438 (pt) cc_final: 0.2206 (tt) REVERT: b 189 ASP cc_start: 0.3979 (p0) cc_final: 0.2816 (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: -0.1740 (ttt) outliers start: 6 outliers final: 2 residues processed: 556 average time/residue: 0.4979 time to fit residues: 422.1605 Evaluate side-chains 266 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 3.258 ------------------------------------------------------------------------------- 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 341 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 317 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 236 optimal weight: 0.0570 chunk 367 optimal weight: 5.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 690 GLN A 703 ASN A 856 ASN A 913 GLN A1048 HIS A1119 ASN B 188 ASN 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 B1048 HIS 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 ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1048 HIS C1083 HIS C1088 HIS C1106 GLN b 171 GLN c 39 GLN c 41 HIS c 52 ASN d 44 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.136991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108866 restraints weight = 121550.088| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.55 r_work: 0.3786 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32791 Z= 0.145 Angle : 0.587 11.313 44645 Z= 0.315 Chirality : 0.044 0.226 5031 Planarity : 0.005 0.070 5754 Dihedral : 4.294 54.945 4391 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.64 % Allowed : 10.33 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4048 helix: -0.93 (0.17), residues: 701 sheet: -0.00 (0.15), residues: 1062 loop : -1.57 (0.11), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 152 HIS 0.007 0.001 HIS A 66 PHE 0.029 0.001 PHE B 32 TYR 0.036 0.002 TYR a 94 ARG 0.010 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 1087) hydrogen bonds : angle 6.37598 ( 3039) SS BOND : bond 0.00454 ( 42) SS BOND : angle 2.29274 ( 84) covalent geometry : bond 0.00315 (32749) covalent geometry : angle 0.57955 (44561) *********************** 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 315 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 256 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8011 (m-80) cc_final: 0.7583 (m-80) REVERT: A 430 THR cc_start: 0.5186 (OUTLIER) cc_final: 0.4965 (t) REVERT: A 562 PHE cc_start: 0.7025 (m-80) cc_final: 0.6482 (m-10) REVERT: A 878 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9185 (tt) REVERT: A 904 TYR cc_start: 0.7169 (t80) cc_final: 0.6923 (t80) REVERT: A 918 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: A 1019 ARG cc_start: 0.8615 (tpt170) cc_final: 0.8184 (tpt170) REVERT: B 77 LYS cc_start: 0.3134 (mmtp) cc_final: 0.1893 (tmtt) REVERT: B 166 CYS cc_start: 0.5024 (OUTLIER) cc_final: 0.4591 (m) REVERT: B 786 LYS cc_start: 0.8266 (ptmm) cc_final: 0.7864 (tptp) REVERT: B 902 MET cc_start: 0.8895 (mmm) cc_final: 0.8648 (mmt) REVERT: B 904 TYR cc_start: 0.7413 (t80) cc_final: 0.7170 (t80) REVERT: C 1010 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7911 (tp40) REVERT: a 203 HIS cc_start: 0.0383 (t-170) cc_final: 0.0063 (t70) REVERT: c 34 MET cc_start: 0.2778 (tpp) cc_final: 0.1271 (mmt) REVERT: c 47 TRP cc_start: 0.3480 (t60) cc_final: 0.2790 (t60) outliers start: 59 outliers final: 26 residues processed: 304 average time/residue: 0.4323 time to fit residues: 210.4257 Evaluate side-chains 223 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL 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 432 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 TYR 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 C residue 1010 GLN Chi-restraints excluded: chain C residue 1050 MET 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 Chi-restraints excluded: chain c residue 155 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 297 optimal weight: 1.9990 chunk 215 optimal weight: 0.0030 chunk 331 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 352 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- 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 703 ASN A 856 ASN B 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 563 GLN C 762 GLN C1005 GLN b 37 ASN c 41 HIS d 44 GLN d 142 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.134894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.106749 restraints weight = 119990.086| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 3.85 r_work: 0.3746 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32791 Z= 0.134 Angle : 0.539 11.315 44645 Z= 0.286 Chirality : 0.043 0.182 5031 Planarity : 0.004 0.048 5754 Dihedral : 4.190 41.201 4391 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.06 % Allowed : 12.12 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4048 helix: 0.73 (0.19), residues: 709 sheet: 0.08 (0.15), residues: 1075 loop : -1.25 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 886 HIS 0.005 0.001 HIS B 146 PHE 0.022 0.001 PHE C 855 TYR 0.022 0.001 TYR A 380 ARG 0.006 0.001 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 1087) hydrogen bonds : angle 5.59015 ( 3039) SS BOND : bond 0.00460 ( 42) SS BOND : angle 1.88569 ( 84) covalent geometry : bond 0.00298 (32749) covalent geometry : angle 0.53298 (44561) *********************** 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 272 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 198 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8047 (m-80) cc_final: 0.7725 (m-80) REVERT: A 301 CYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8129 (m) REVERT: A 451 TYR cc_start: 0.3769 (m-80) cc_final: 0.3094 (t80) REVERT: A 979 ASP cc_start: 0.8853 (t0) cc_final: 0.8530 (t0) REVERT: A 1019 ARG cc_start: 0.8676 (tpt170) cc_final: 0.8155 (tpt170) REVERT: B 98 SER cc_start: 0.4387 (p) cc_final: 0.3835 (t) REVERT: B 773 GLU cc_start: 0.8860 (tt0) cc_final: 0.8450 (tt0) REVERT: B 902 MET cc_start: 0.8927 (mmm) cc_final: 0.8620 (mmt) REVERT: B 1041 ASP cc_start: 0.7924 (t0) cc_final: 0.7698 (t0) REVERT: C 856 ASN cc_start: 0.8366 (t0) cc_final: 0.8134 (t0) REVERT: a 185 VAL cc_start: 0.3457 (OUTLIER) cc_final: 0.3236 (m) REVERT: a 203 HIS cc_start: -0.0010 (t-170) cc_final: -0.0290 (t70) REVERT: c 34 MET cc_start: 0.2185 (tpp) cc_final: -0.0308 (mmt) REVERT: c 36 TRP cc_start: 0.2389 (m100) cc_final: 0.1054 (m100) outliers start: 74 outliers final: 36 residues processed: 261 average time/residue: 0.4343 time to fit residues: 190.5987 Evaluate side-chains 211 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 453 TYR 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 915 VAL 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 320 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 324 GLU 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 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 185 VAL 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 44 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 316 optimal weight: 0.6980 chunk 389 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 379 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 185 ASN B 703 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C1002 GLN C1005 GLN C1011 GLN b 95 GLN b 129 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 = 0.4384 r_free = 0.4384 target = 0.131806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.103983 restraints weight = 119730.833| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 4.19 r_work: 0.3684 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32791 Z= 0.175 Angle : 0.591 11.621 44645 Z= 0.312 Chirality : 0.044 0.215 5031 Planarity : 0.004 0.049 5754 Dihedral : 4.508 44.866 4389 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.70 % Allowed : 13.90 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4048 helix: 1.28 (0.20), residues: 718 sheet: 0.03 (0.15), residues: 1062 loop : -1.14 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP c 47 HIS 0.006 0.001 HIS A1064 PHE 0.023 0.002 PHE B 855 TYR 0.023 0.002 TYR d 55 ARG 0.006 0.001 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 1087) hydrogen bonds : angle 5.45051 ( 3039) SS BOND : bond 0.00595 ( 42) SS BOND : angle 2.28640 ( 84) covalent geometry : bond 0.00400 (32749) covalent geometry : angle 0.58324 (44561) *********************** 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 283 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 186 time to evaluate : 3.269 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: 0.7840 (m-80) cc_final: 0.7458 (m-80) REVERT: A 759 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 878 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9267 (tt) REVERT: A 979 ASP cc_start: 0.8945 (t0) cc_final: 0.8670 (t0) REVERT: A 1019 ARG cc_start: 0.8744 (tpt170) cc_final: 0.8227 (tpt170) REVERT: B 421 TYR cc_start: 0.4426 (OUTLIER) cc_final: 0.4128 (m-80) REVERT: B 773 GLU cc_start: 0.8781 (tt0) cc_final: 0.8501 (tt0) REVERT: B 1041 ASP cc_start: 0.8085 (t0) cc_final: 0.7804 (t0) REVERT: C 353 TRP cc_start: -0.1426 (p90) cc_final: -0.1801 (p90) REVERT: a 83 PHE cc_start: -0.0980 (OUTLIER) cc_final: -0.1511 (m-80) REVERT: a 185 VAL cc_start: 0.3484 (OUTLIER) cc_final: 0.3273 (m) REVERT: b 170 ASP cc_start: 0.2112 (p0) cc_final: 0.1489 (t0) REVERT: c 34 MET cc_start: 0.1677 (tpp) cc_final: 0.0174 (mmt) REVERT: c 36 TRP cc_start: 0.1760 (m100) cc_final: 0.1487 (m100) REVERT: c 47 TRP cc_start: 0.3172 (t60) cc_final: 0.2290 (t60) outliers start: 97 outliers final: 58 residues processed: 259 average time/residue: 0.3930 time to fit residues: 170.8754 Evaluate side-chains 234 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 171 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET 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 380 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 453 TYR 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 878 LEU 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 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 421 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 736 VAL 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 47 VAL Chi-restraints excluded: chain C residue 129 LYS 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 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 1005 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET 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 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 155 THR Chi-restraints excluded: chain c residue 169 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 40 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 279 optimal weight: 0.6980 chunk 381 optimal weight: 1.9990 chunk 274 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 762 GLN C1005 GLN b 95 GLN c 41 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.132677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.105583 restraints weight = 119994.803| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.11 r_work: 0.3695 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32791 Z= 0.102 Angle : 0.499 10.337 44645 Z= 0.262 Chirality : 0.042 0.182 5031 Planarity : 0.004 0.045 5754 Dihedral : 4.158 43.231 4389 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.01 % Allowed : 15.54 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4048 helix: 1.78 (0.20), residues: 716 sheet: 0.14 (0.15), residues: 1084 loop : -1.00 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 886 HIS 0.003 0.001 HIS A 655 PHE 0.041 0.001 PHE B 855 TYR 0.023 0.001 TYR A 451 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1087) hydrogen bonds : angle 5.14899 ( 3039) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.68021 ( 84) covalent geometry : bond 0.00227 (32749) covalent geometry : angle 0.49404 (44561) *********************** 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 260 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 3.233 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 878 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9268 (tt) REVERT: A 979 ASP cc_start: 0.8872 (t0) cc_final: 0.8639 (t0) REVERT: A 1019 ARG cc_start: 0.8805 (tpt170) cc_final: 0.8292 (tpt170) REVERT: B 104 TRP cc_start: 0.7526 (m-90) cc_final: 0.7078 (m-90) REVERT: B 335 LEU cc_start: 0.2658 (mt) cc_final: 0.2452 (pt) REVERT: B 773 GLU cc_start: 0.8699 (tt0) cc_final: 0.8430 (tt0) REVERT: B 1041 ASP cc_start: 0.8000 (t0) cc_final: 0.7719 (t0) REVERT: a 83 PHE cc_start: -0.0427 (OUTLIER) cc_final: -0.1192 (t80) REVERT: b 104 PHE cc_start: 0.0621 (OUTLIER) cc_final: -0.0295 (t80) REVERT: b 189 ASP cc_start: 0.3379 (p0) cc_final: 0.2687 (m-30) REVERT: c 34 MET cc_start: 0.1478 (tpp) cc_final: 0.0050 (mmt) REVERT: c 36 TRP cc_start: 0.1714 (m100) cc_final: 0.1420 (m100) outliers start: 72 outliers final: 43 residues processed: 246 average time/residue: 0.4161 time to fit residues: 175.4414 Evaluate side-chains 214 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 430 THR Chi-restraints excluded: chain A residue 432 CYS 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 878 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1128 VAL 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 398 ASP 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 B residue 955 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 129 LYS 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 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR 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 83 PHE Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 120 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 71 THR Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain d residue 120 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 280 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 chunk 403 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 327 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 856 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN C 762 GLN a 41 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.132619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.104634 restraints weight = 120481.813| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.93 r_work: 0.3708 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 32791 Z= 0.101 Angle : 0.495 12.982 44645 Z= 0.259 Chirality : 0.042 0.181 5031 Planarity : 0.004 0.048 5754 Dihedral : 4.047 42.368 4389 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.34 % Allowed : 16.13 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 4048 helix: 2.00 (0.20), residues: 717 sheet: 0.24 (0.15), residues: 1071 loop : -0.94 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP c 47 HIS 0.003 0.001 HIS B 146 PHE 0.017 0.001 PHE C 133 TYR 0.029 0.001 TYR A 453 ARG 0.003 0.000 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 1087) hydrogen bonds : angle 5.02576 ( 3039) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.62796 ( 84) covalent geometry : bond 0.00225 (32749) covalent geometry : angle 0.49051 (44561) *********************** 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 268 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 184 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5127 (tpp-160) REVERT: A 878 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9256 (tt) REVERT: A 979 ASP cc_start: 0.8902 (t0) cc_final: 0.8698 (t0) REVERT: A 1019 ARG cc_start: 0.8748 (tpt170) cc_final: 0.8273 (tpt170) REVERT: B 104 TRP cc_start: 0.7571 (m-90) cc_final: 0.7138 (m-90) REVERT: B 773 GLU cc_start: 0.8650 (tt0) cc_final: 0.8382 (tt0) REVERT: C 759 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7821 (t80) REVERT: a 83 PHE cc_start: -0.0317 (OUTLIER) cc_final: -0.1423 (m-80) REVERT: b 104 PHE cc_start: 0.0599 (OUTLIER) cc_final: -0.0300 (t80) REVERT: b 189 ASP cc_start: 0.3828 (p0) cc_final: 0.3157 (m-30) REVERT: c 34 MET cc_start: 0.1519 (tpp) cc_final: 0.1161 (ttm) outliers start: 84 outliers final: 55 residues processed: 250 average time/residue: 0.4272 time to fit residues: 182.3408 Evaluate side-chains 232 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 3.618 ------------------------------------------------------------------------------- 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 214 ARG 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 430 THR Chi-restraints excluded: chain A residue 432 CYS 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 858 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1128 VAL 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 398 ASP 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 129 LYS 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 559 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 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 2 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 83 PHE 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 186 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 252 optimal weight: 0.0050 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 390 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 342 optimal weight: 0.5980 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 762 GLN B 935 GLN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.141566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.106789 restraints weight = 128177.117| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 4.80 r_work: 0.3696 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32791 Z= 0.090 Angle : 0.480 12.782 44645 Z= 0.251 Chirality : 0.042 0.174 5031 Planarity : 0.003 0.047 5754 Dihedral : 3.945 42.131 4389 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.14 % Allowed : 16.77 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4048 helix: 2.22 (0.20), residues: 716 sheet: 0.34 (0.15), residues: 1070 loop : -0.87 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP c 47 HIS 0.003 0.000 HIS B 146 PHE 0.021 0.001 PHE a 106 TYR 0.018 0.001 TYR d 55 ARG 0.003 0.000 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1087) hydrogen bonds : angle 4.83605 ( 3039) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.90478 ( 84) covalent geometry : bond 0.00198 (32749) covalent geometry : angle 0.47302 (44561) *********************** 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 263 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 186 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3555 (ttm) cc_final: 0.3332 (ttt) REVERT: A 214 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5584 (mmm160) REVERT: A 878 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9242 (tt) REVERT: A 979 ASP cc_start: 0.8925 (t0) cc_final: 0.8689 (t0) REVERT: A 1019 ARG cc_start: 0.8749 (tpt170) cc_final: 0.8255 (tpt170) REVERT: B 104 TRP cc_start: 0.7583 (m-90) cc_final: 0.7132 (m-90) REVERT: B 773 GLU cc_start: 0.8713 (tt0) cc_final: 0.8401 (tt0) REVERT: C 759 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7927 (t80) REVERT: a 34 MET cc_start: 0.3783 (tpt) cc_final: 0.0543 (ptm) REVERT: a 51 ILE cc_start: 0.3453 (tt) cc_final: 0.2183 (tt) REVERT: a 83 PHE cc_start: 0.0041 (OUTLIER) cc_final: -0.0951 (m-80) REVERT: b 104 PHE cc_start: 0.1109 (OUTLIER) cc_final: 0.0055 (t80) REVERT: b 170 ASP cc_start: 0.2632 (p0) cc_final: 0.1721 (t0) REVERT: b 189 ASP cc_start: 0.4110 (p0) cc_final: 0.3378 (m-30) outliers start: 77 outliers final: 56 residues processed: 246 average time/residue: 0.4139 time to fit residues: 174.2309 Evaluate side-chains 235 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 3.203 ------------------------------------------------------------------------------- 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 214 ARG 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 380 TYR Chi-restraints excluded: chain A residue 432 CYS 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 760 CYS Chi-restraints excluded: chain A residue 858 LEU 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 1034 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL 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 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 759 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 125 VAL Chi-restraints excluded: chain a residue 186 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 71 THR Chi-restraints excluded: chain c residue 83 PHE Chi-restraints excluded: chain c residue 140 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 258 optimal weight: 0.4980 chunk 337 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 356 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 393 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN B1002 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.106094 restraints weight = 127021.393| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.75 r_work: 0.3682 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32791 Z= 0.110 Angle : 0.500 12.692 44645 Z= 0.260 Chirality : 0.042 0.168 5031 Planarity : 0.004 0.054 5754 Dihedral : 3.999 42.163 4389 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.56 % Allowed : 16.82 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4048 helix: 2.22 (0.20), residues: 718 sheet: 0.32 (0.15), residues: 1078 loop : -0.85 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 886 HIS 0.004 0.001 HIS B 146 PHE 0.012 0.001 PHE A 562 TYR 0.018 0.001 TYR d 55 ARG 0.003 0.000 ARG C 995 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 1087) hydrogen bonds : angle 4.82334 ( 3039) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.82882 ( 84) covalent geometry : bond 0.00249 (32749) covalent geometry : angle 0.49405 (44561) *********************** 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 273 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 181 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3649 (ttm) cc_final: 0.3404 (ttt) REVERT: A 214 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5519 (mmm160) REVERT: A 229 LEU cc_start: 0.7888 (mt) cc_final: 0.7553 (mt) REVERT: A 878 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9238 (tt) REVERT: A 960 ASN cc_start: 0.9299 (OUTLIER) cc_final: 0.9083 (t0) REVERT: A 979 ASP cc_start: 0.8964 (t0) cc_final: 0.8729 (t0) REVERT: A 1019 ARG cc_start: 0.8756 (tpt170) cc_final: 0.8181 (tpt170) REVERT: B 773 GLU cc_start: 0.8733 (tt0) cc_final: 0.8409 (tt0) REVERT: C 759 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8053 (t80) REVERT: a 83 PHE cc_start: 0.0540 (OUTLIER) cc_final: -0.1297 (m-80) REVERT: a 94 TYR cc_start: 0.2049 (m-80) cc_final: 0.0907 (m-80) REVERT: b 104 PHE cc_start: 0.1340 (OUTLIER) cc_final: 0.0298 (t80) REVERT: b 189 ASP cc_start: 0.4159 (p0) cc_final: 0.3414 (m-30) REVERT: c 199 CYS cc_start: -0.1321 (OUTLIER) cc_final: -0.1783 (p) outliers start: 92 outliers final: 68 residues processed: 254 average time/residue: 0.3948 time to fit residues: 171.3444 Evaluate side-chains 246 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 171 time to evaluate : 3.622 ------------------------------------------------------------------------------- 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 214 ARG 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 432 CYS 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 760 CYS Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1128 VAL 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 398 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL 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 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 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 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 C residue 1092 GLU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 83 PHE 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 141 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 62 SER 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 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 c residue 199 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 13 optimal weight: 8.9990 chunk 388 optimal weight: 3.9990 chunk 295 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 284 optimal weight: 4.9990 chunk 404 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 655 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 907 ASN B 913 GLN B 914 ASN C 185 ASN C 762 GLN C 804 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102029 restraints weight = 119486.573| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.70 r_work: 0.3693 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32791 Z= 0.173 Angle : 0.591 13.852 44645 Z= 0.308 Chirality : 0.044 0.170 5031 Planarity : 0.004 0.050 5754 Dihedral : 4.480 44.114 4389 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.45 % Allowed : 17.05 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4048 helix: 2.08 (0.20), residues: 711 sheet: 0.24 (0.15), residues: 1059 loop : -1.00 (0.13), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP c 47 HIS 0.006 0.001 HIS A1064 PHE 0.045 0.002 PHE B 906 TYR 0.019 0.002 TYR d 55 ARG 0.007 0.001 ARG a 98 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1087) hydrogen bonds : angle 5.22354 ( 3039) SS BOND : bond 0.00457 ( 42) SS BOND : angle 1.88906 ( 84) covalent geometry : bond 0.00393 (32749) covalent geometry : angle 0.58599 (44561) *********************** 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 270 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 182 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9229 (tt) REVERT: A 960 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.9083 (t0) REVERT: A 1019 ARG cc_start: 0.8760 (tpt170) cc_final: 0.8201 (tpt170) REVERT: B 421 TYR cc_start: 0.4048 (OUTLIER) cc_final: 0.3620 (m-80) REVERT: B 773 GLU cc_start: 0.8660 (tt0) cc_final: 0.8324 (tt0) REVERT: C 353 TRP cc_start: -0.1194 (p90) cc_final: -0.1949 (p90) REVERT: C 759 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7890 (t80) REVERT: a 10 GLU cc_start: 0.0629 (mp0) cc_final: -0.1111 (tp30) REVERT: a 34 MET cc_start: 0.3413 (tpt) cc_final: 0.0305 (ptm) REVERT: a 83 PHE cc_start: 0.0288 (OUTLIER) cc_final: -0.1320 (m-80) REVERT: b 104 PHE cc_start: 0.2560 (OUTLIER) cc_final: 0.1525 (t80) REVERT: b 166 ASN cc_start: 0.3308 (m-40) cc_final: 0.2971 (t0) REVERT: b 189 ASP cc_start: 0.3771 (p0) cc_final: 0.2862 (m-30) REVERT: c 34 MET cc_start: 0.2566 (tpt) cc_final: -0.0456 (mpp) REVERT: c 199 CYS cc_start: -0.3031 (OUTLIER) cc_final: -0.3306 (p) outliers start: 88 outliers final: 65 residues processed: 251 average time/residue: 0.3965 time to fit residues: 169.7054 Evaluate side-chains 237 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 3.434 ------------------------------------------------------------------------------- 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 318 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS 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 760 CYS Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP 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 347 PHE 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 662 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL 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 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 83 PHE 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 186 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 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 199 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 57 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 302 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 954 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1159 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 = 0.4357 r_free = 0.4357 target = 0.130516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.104055 restraints weight = 119908.155| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.85 r_work: 0.3673 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5579 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= 0.123 Angle : 0.539 12.737 44645 Z= 0.280 Chirality : 0.043 0.231 5031 Planarity : 0.004 0.066 5754 Dihedral : 4.311 42.323 4389 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.20 % Allowed : 17.33 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4048 helix: 2.19 (0.20), residues: 709 sheet: 0.31 (0.15), residues: 1063 loop : -1.00 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 886 HIS 0.004 0.001 HIS B 146 PHE 0.061 0.001 PHE b 214 TYR 0.020 0.001 TYR d 55 ARG 0.010 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1087) hydrogen bonds : angle 5.02985 ( 3039) SS BOND : bond 0.00403 ( 42) SS BOND : angle 2.06783 ( 84) covalent geometry : bond 0.00280 (32749) covalent geometry : angle 0.53173 (44561) ********************** 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 251 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 3.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9230 (tt) REVERT: A 960 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9106 (t0) REVERT: A 1019 ARG cc_start: 0.8799 (tpt170) cc_final: 0.8230 (tpt170) REVERT: B 177 MET cc_start: -0.1302 (mmp) cc_final: -0.1582 (mmp) REVERT: B 421 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.3940 (m-80) REVERT: B 773 GLU cc_start: 0.8725 (tt0) cc_final: 0.8392 (tt0) REVERT: B 1002 GLN cc_start: 0.8634 (tt0) cc_final: 0.8366 (tm-30) REVERT: C 759 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8031 (t80) REVERT: a 10 GLU cc_start: 0.0519 (mp0) cc_final: -0.1157 (tp30) REVERT: a 34 MET cc_start: 0.2851 (tpt) cc_final: -0.0172 (ptm) REVERT: a 83 PHE cc_start: 0.0163 (OUTLIER) cc_final: -0.1229 (m-80) REVERT: b 104 PHE cc_start: 0.2477 (OUTLIER) cc_final: 0.1619 (t80) REVERT: b 189 ASP cc_start: 0.3899 (p0) cc_final: 0.3107 (m-30) REVERT: c 199 CYS cc_start: -0.1964 (OUTLIER) cc_final: -0.2619 (p) outliers start: 79 outliers final: 67 residues processed: 238 average time/residue: 0.3974 time to fit residues: 161.4105 Evaluate side-chains 242 residues out of total 3592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 168 time to evaluate : 3.391 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 CYS 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 760 CYS 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 960 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 64 TRP 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 347 PHE 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 662 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 47 VAL 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 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 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 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 83 PHE 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 178 LEU Chi-restraints excluded: chain a residue 186 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 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 199 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 148 optimal weight: 3.9990 chunk 398 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 399 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.128698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.100572 restraints weight = 117700.089| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.83 r_work: 0.3662 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32791 Z= 0.174 Angle : 0.601 13.059 44645 Z= 0.313 Chirality : 0.045 0.167 5031 Planarity : 0.004 0.060 5754 Dihedral : 4.608 43.285 4389 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.28 % Allowed : 17.47 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.94 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4048 helix: 1.96 (0.20), residues: 718 sheet: 0.11 (0.15), residues: 1086 loop : -1.11 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP C 886 HIS 0.006 0.001 HIS a 168 PHE 0.037 0.002 PHE b 214 TYR 0.047 0.002 TYR A 904 ARG 0.008 0.001 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1087) hydrogen bonds : angle 5.25680 ( 3039) SS BOND : bond 0.00420 ( 42) SS BOND : angle 2.19862 ( 84) covalent geometry : bond 0.00399 (32749) covalent geometry : angle 0.59381 (44561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24002.57 seconds wall clock time: 413 minutes 33.11 seconds (24813.11 seconds total)