Starting phenix.real_space_refine on Fri Mar 6 18:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7faf_31503/03_2026/7faf_31503.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 144 5.16 5 C 21140 2.51 5 N 5558 2.21 5 O 6446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33288 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7767 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 943} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "c" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "d" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "f" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "g" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7743 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 941} Chain breaks: 10 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.48, per 1000 atoms: 0.22 Number of scatterers: 33288 At special positions: 0 Unit cell: (220.19, 184.3, 182.36, 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 144 16.00 O 6446 8.00 N 5558 7.00 C 21140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.02 Simple disulfide: pdb=" SG CYS H 168 " - pdb=" SG CYS H 224 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.04 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 213 " distance=2.04 Simple disulfide: pdb=" SG CYS c 42 " - pdb=" SG CYS c 107 " distance=2.04 Simple disulfide: pdb=" SG CYS c 153 " - pdb=" SG CYS c 213 " distance=2.04 Simple disulfide: pdb=" SG CYS d 41 " - pdb=" SG CYS d 115 " distance=2.02 Simple disulfide: pdb=" SG CYS d 168 " - pdb=" SG CYS d 224 " distance=2.03 Simple disulfide: pdb=" SG CYS f 42 " - pdb=" SG CYS f 107 " distance=2.04 Simple disulfide: pdb=" SG CYS f 153 " - pdb=" SG CYS f 213 " distance=2.04 Simple disulfide: pdb=" SG CYS g 41 " - pdb=" SG CYS g 115 " distance=2.02 Simple disulfide: pdb=" SG CYS g 168 " - pdb=" SG CYS g 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.02 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=1.99 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 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.94 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 73 sheets defined 20.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.566A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.830A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.654A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.665A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 783 removed outlier: 3.766A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.929A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.726A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 965 removed outlier: 4.092A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.417A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.684A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.565A pdb=" N THR H 159 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 229 through 232 Processing helix chain 'L' and resid 98 through 102 Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU L 206 " --> pdb=" O LYS L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 202 through 206' Processing helix chain 'c' and resid 98 through 102 Processing helix chain 'c' and resid 140 through 145 Processing helix chain 'c' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU c 206 " --> pdb=" O LYS c 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 202 through 206' Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 155 through 159 removed outlier: 3.564A pdb=" N THR d 159 " --> pdb=" O SER d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 215 through 217 No H-bonds generated for 'chain 'd' and resid 215 through 217' Processing helix chain 'd' and resid 229 through 232 Processing helix chain 'f' and resid 98 through 102 Processing helix chain 'f' and resid 140 through 145 Processing helix chain 'f' and resid 202 through 206 removed outlier: 3.749A pdb=" N GLU f 206 " --> pdb=" O LYS f 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 202 through 206' Processing helix chain 'g' and resid 106 through 110 Processing helix chain 'g' and resid 155 through 159 removed outlier: 3.565A pdb=" N THR g 159 " --> pdb=" O SER g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 215 through 217 No H-bonds generated for 'chain 'g' and resid 215 through 217' Processing helix chain 'g' and resid 229 through 232 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.495A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.549A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.611A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 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 783 removed outlier: 3.880A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.134A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.553A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.569A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 980 removed outlier: 3.640A pdb=" N ILE B 980 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.400A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.683A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.757A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.132A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.964A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 410' Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.666A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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 783 removed outlier: 3.766A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.574A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.527A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.929A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.601A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.566A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.531A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.685A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.041A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.720A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.775A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.433A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.883A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.566A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.880A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.248A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.248A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.518A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AB6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU H 29 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER H 208 " --> pdb=" O CYS H 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR H 204 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER H 208 " --> pdb=" O CYS H 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR H 204 " --> pdb=" O ASP H 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 205 " --> pdb=" O VAL H 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.781A pdb=" N CYS H 224 " --> pdb=" O LYS H 237 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 237 " --> pdb=" O CYS H 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 23 through 26 removed outlier: 3.645A pdb=" N THR L 91 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 72 through 73 removed outlier: 6.381A pdb=" N TRP L 54 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR L 68 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU L 52 " --> pdb=" O TYR L 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR L 192 " --> pdb=" O ASN L 157 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 173 through 174 removed outlier: 4.707A pdb=" N TRP L 167 " --> pdb=" O GLN L 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 23 through 26 removed outlier: 3.644A pdb=" N THR c 91 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 72 through 73 removed outlier: 6.381A pdb=" N TRP c 54 " --> pdb=" O LEU c 66 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR c 68 " --> pdb=" O LEU c 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU c 52 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR c 192 " --> pdb=" O ASN c 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'c' and resid 173 through 174 removed outlier: 4.708A pdb=" N TRP c 167 " --> pdb=" O GLN c 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 22 through 25 Processing sheet with id=AD1, first strand: chain 'd' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU d 29 " --> pdb=" O THR d 138 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG d 57 " --> pdb=" O TRP d 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP d 66 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 148 through 152 removed outlier: 3.660A pdb=" N SER d 208 " --> pdb=" O CYS d 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR d 204 " --> pdb=" O ASP d 172 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 148 through 152 removed outlier: 3.660A pdb=" N SER d 208 " --> pdb=" O CYS d 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR d 204 " --> pdb=" O ASP d 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER d 205 " --> pdb=" O VAL d 197 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 179 through 182 removed outlier: 3.780A pdb=" N CYS d 224 " --> pdb=" O LYS d 237 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS d 237 " --> pdb=" O CYS d 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 23 through 26 removed outlier: 3.644A pdb=" N THR f 91 " --> pdb=" O SER f 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 72 through 73 removed outlier: 6.380A pdb=" N TRP f 54 " --> pdb=" O LEU f 66 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR f 68 " --> pdb=" O LEU f 52 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU f 52 " --> pdb=" O TYR f 68 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 133 through 137 removed outlier: 5.625A pdb=" N TYR f 192 " --> pdb=" O ASN f 157 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'f' and resid 173 through 174 removed outlier: 4.708A pdb=" N TRP f 167 " --> pdb=" O GLN f 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 22 through 25 Processing sheet with id=AE1, first strand: chain 'g' and resid 29 through 31 removed outlier: 6.876A pdb=" N GLU g 29 " --> pdb=" O THR g 138 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG g 57 " --> pdb=" O TRP g 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP g 66 " --> pdb=" O ARG g 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER g 208 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR g 204 " --> pdb=" O ASP g 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 148 through 152 removed outlier: 3.658A pdb=" N SER g 208 " --> pdb=" O CYS g 168 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR g 204 " --> pdb=" O ASP g 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER g 205 " --> pdb=" O VAL g 197 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'g' and resid 179 through 182 removed outlier: 3.781A pdb=" N CYS g 224 " --> pdb=" O LYS g 237 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS g 237 " --> pdb=" O CYS g 224 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.835A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.835A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.169A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.518A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.098A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.883A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 323 through 328 removed outlier: 7.008A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.784A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.613A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 713 through 723 removed outlier: 6.915A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 713 through 723 removed outlier: 6.915A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.411A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AG2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.759A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AG4, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.806A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 117 through 121 removed outlier: 7.167A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=AG7, first strand: chain 'C' and resid 188 through 193 removed outlier: 3.548A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.432A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 323 through 327 removed outlier: 4.251A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.615A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'C' and resid 551 through 552 removed outlier: 3.776A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.534A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.092A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.092A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.519A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1120 through 1122 1306 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10277 1.34 - 1.48: 8573 1.48 - 1.63: 15005 1.63 - 1.78: 24 1.78 - 1.92: 168 Bond restraints: 34047 Sorted by residual: bond pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 1.520 1.616 -0.096 1.42e-02 4.96e+03 4.60e+01 bond pdb=" CB THR d 219 " pdb=" CG2 THR d 219 " ideal model delta sigma weight residual 1.521 1.699 -0.178 3.30e-02 9.18e+02 2.91e+01 bond pdb=" CB THR H 219 " pdb=" CG2 THR H 219 " ideal model delta sigma weight residual 1.521 1.699 -0.178 3.30e-02 9.18e+02 2.90e+01 bond pdb=" CB THR g 219 " pdb=" CG2 THR g 219 " ideal model delta sigma weight residual 1.521 1.698 -0.177 3.30e-02 9.18e+02 2.88e+01 bond pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " ideal model delta sigma weight residual 1.520 1.362 0.158 3.00e-02 1.11e+03 2.77e+01 ... (remaining 34042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.18: 46126 9.18 - 18.35: 167 18.35 - 27.53: 15 27.53 - 36.71: 0 36.71 - 45.88: 15 Bond angle restraints: 46323 Sorted by residual: angle pdb=" C LEU A 533 " pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 122.95 100.24 22.71 1.24e+00 6.50e-01 3.35e+02 angle pdb=" CB LYS L 188 " pdb=" CG LYS L 188 " pdb=" CD LYS L 188 " ideal model delta sigma weight residual 111.30 71.84 39.46 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LYS c 188 " pdb=" CG LYS c 188 " pdb=" CD LYS c 188 " ideal model delta sigma weight residual 111.30 71.85 39.45 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LYS f 188 " pdb=" CG LYS f 188 " pdb=" CD LYS f 188 " ideal model delta sigma weight residual 111.30 71.86 39.44 2.30e+00 1.89e-01 2.94e+02 angle pdb=" CB LEU g 102 " pdb=" CG LEU g 102 " pdb=" CD1 LEU g 102 " ideal model delta sigma weight residual 110.70 156.58 -45.88 3.00e+00 1.11e-01 2.34e+02 ... (remaining 46318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17582 17.95 - 35.91: 1687 35.91 - 53.86: 788 53.86 - 71.82: 214 71.82 - 89.77: 60 Dihedral angle restraints: 20331 sinusoidal: 7863 harmonic: 12468 Sorted by residual: dihedral pdb=" CA VAL B 382 " pdb=" C VAL B 382 " pdb=" N SER B 383 " pdb=" CA SER B 383 " ideal model delta harmonic sigma weight residual -180.00 -102.72 -77.28 0 5.00e+00 4.00e-02 2.39e+02 dihedral pdb=" CA TYR f 113 " pdb=" C TYR f 113 " pdb=" N PRO f 114 " pdb=" CA PRO f 114 " ideal model delta harmonic sigma weight residual -180.00 -117.26 -62.74 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA TYR c 113 " pdb=" C TYR c 113 " pdb=" N PRO c 114 " pdb=" CA PRO c 114 " ideal model delta harmonic sigma weight residual -180.00 -117.33 -62.67 0 5.00e+00 4.00e-02 1.57e+02 ... (remaining 20328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.269: 5173 0.269 - 0.537: 50 0.537 - 0.806: 15 0.806 - 1.075: 3 1.075 - 1.344: 3 Chirality restraints: 5244 Sorted by residual: chirality pdb=" CG LEU g 102 " pdb=" CB LEU g 102 " pdb=" CD1 LEU g 102 " pdb=" CD2 LEU g 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.51e+01 chirality pdb=" CG LEU d 102 " pdb=" CB LEU d 102 " pdb=" CD1 LEU d 102 " pdb=" CD2 LEU d 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.50e+01 chirality pdb=" CG LEU H 102 " pdb=" CB LEU H 102 " pdb=" CD1 LEU H 102 " pdb=" CD2 LEU H 102 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.50e+01 ... (remaining 5241 not shown) Planarity restraints: 5989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP f 51 " -0.056 2.00e-02 2.50e+03 4.58e-02 5.25e+01 pdb=" CG TRP f 51 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP f 51 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP f 51 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP f 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP f 51 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP f 51 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 51 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 51 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP f 51 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 51 " -0.056 2.00e-02 2.50e+03 4.57e-02 5.21e+01 pdb=" CG TRP c 51 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP c 51 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP c 51 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP c 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP c 51 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP c 51 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 51 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 51 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP c 51 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 51 " 0.056 2.00e-02 2.50e+03 4.55e-02 5.18e+01 pdb=" CG TRP L 51 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 TRP L 51 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP L 51 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 51 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 51 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 51 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP L 51 " 0.007 2.00e-02 2.50e+03 ... (remaining 5986 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 98 2.33 - 2.97: 17126 2.97 - 3.61: 48829 3.61 - 4.26: 79597 4.26 - 4.90: 127508 Nonbonded interactions: 273158 Sorted by model distance: nonbonded pdb=" CE1 PHE C 133 " pdb=" CB ALA C 163 " model vdw 1.684 3.760 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN B 394 " model vdw 1.933 3.120 nonbonded pdb=" NE2 GLN f 166 " pdb=" OE1 GLU f 214 " model vdw 1.970 3.120 nonbonded pdb=" NE2 GLN L 166 " pdb=" OE1 GLU L 214 " model vdw 1.970 3.120 nonbonded pdb=" NE2 GLN c 166 " pdb=" OE1 GLU c 214 " model vdw 1.970 3.120 ... (remaining 273153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 228 or (resid 229 \ and (name N or name CA or name C or name O or name CB )) or resid 230 through 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 through 274 or (resid 275 and (name N or name CA or name C or name O or na \ me CB )) or resid 276 through 327 or (resid 328 and (name N or name CA or name C \ or name O or name CB )) or resid 329 through 514 or resid 524 through 528 or (r \ esid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 t \ hrough 543 or resid 549 through 1146)) selection = (chain 'B' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 199 or (resid 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 228 o \ r (resid 229 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 30 through 232 or (resid 233 and (name N or name CA or name C or name O or name \ CB )) or resid 234 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 327 or (resid 328 and (name N or name \ CA or name C or name O or name CB )) or resid 329 through 514 or resid 524 thro \ ugh 527 or (resid 528 through 529 and (name N or name CA or name C or name O or \ name CB )) or resid 530 through 543 or resid 549 through 564 or (resid 565 and ( \ name N or name CA or name C or name O or name CB )) or resid 566 or (resid 567 a \ nd (name N or name CA or name C or name O or name CB )) or resid 568 through 940 \ or resid 946 through 1146)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 514 or resid 524 through 564 or (r \ esid 565 and (name N or name CA or name C or name O or name CB )) or resid 566 o \ r (resid 567 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 68 through 940 or resid 946 through 1146)) } ncs_group { reference = chain 'H' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'L' selection = chain 'c' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.870 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 0.011 0.178 34099 Z= 0.661 Angle : 1.812 45.884 46425 Z= 1.063 Chirality : 0.101 1.344 5244 Planarity : 0.009 0.139 5989 Dihedral : 18.609 89.772 12166 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.32 % Favored : 88.76 % Rotamer: Outliers : 13.67 % Allowed : 6.38 % Favored : 79.96 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 4.93 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.12), residues: 4226 helix: -1.54 (0.17), residues: 702 sheet: -1.61 (0.15), residues: 1110 loop : -2.60 (0.11), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.003 ARG f 161 TYR 0.083 0.004 TYR f 113 PHE 0.101 0.004 PHE g 128 TRP 0.123 0.006 TRP f 51 HIS 0.011 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.01088 (34047) covalent geometry : angle 1.80759 (46323) SS BOND : bond 0.01711 ( 51) SS BOND : angle 3.14316 ( 102) hydrogen bonds : bond 0.16893 ( 1212) hydrogen bonds : angle 9.33498 ( 3456) Misc. bond : bond 0.11516 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 510 poor density : 822 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6596 (p0) REVERT: A 368 LEU cc_start: 0.7094 (mp) cc_final: 0.6709 (tp) REVERT: A 529 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5612 (mmmt) REVERT: A 564 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: A 752 LEU cc_start: 0.8591 (mt) cc_final: 0.7558 (mm) REVERT: A 816 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9090 (t) REVERT: A 1104 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8624 (t) REVERT: A 1133 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7604 (t) REVERT: H 76 ASN cc_start: 0.7762 (m-40) cc_final: 0.7360 (t0) REVERT: H 99 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5364 (m-10) REVERT: H 133 GLN cc_start: 0.4553 (OUTLIER) cc_final: 0.3502 (tp40) REVERT: L 106 TYR cc_start: 0.2600 (m-80) cc_final: 0.2325 (m-10) REVERT: L 206 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5158 (mp0) REVERT: c 23 MET cc_start: 0.2410 (mtp) cc_final: 0.2078 (mmm) REVERT: c 66 LEU cc_start: 0.2507 (OUTLIER) cc_final: 0.1819 (mp) REVERT: c 202 LYS cc_start: 0.1974 (mmtm) cc_final: 0.0229 (tptt) REVERT: c 206 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2984 (mp0) REVERT: c 230 ARG cc_start: 0.4314 (OUTLIER) cc_final: 0.2754 (mmp80) REVERT: d 22 GLN cc_start: 0.4304 (OUTLIER) cc_final: 0.3979 (tp-100) REVERT: d 79 TYR cc_start: 0.1186 (m-80) cc_final: 0.0917 (m-80) REVERT: d 216 SER cc_start: 0.4112 (OUTLIER) cc_final: 0.3797 (t) REVERT: f 73 LEU cc_start: 0.6964 (tp) cc_final: 0.6718 (tt) REVERT: f 141 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6614 (p0) REVERT: f 205 TYR cc_start: -0.0958 (t80) cc_final: -0.1233 (t80) REVERT: g 108 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5256 (pm20) REVERT: g 109 ASP cc_start: 0.6951 (m-30) cc_final: 0.5660 (t70) REVERT: g 113 TYR cc_start: 0.5697 (m-80) cc_final: 0.5184 (m-10) REVERT: B 101 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5050 (pt) REVERT: B 540 ASN cc_start: 0.3015 (OUTLIER) cc_final: 0.1841 (t0) REVERT: B 816 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8499 (t) REVERT: B 823 PHE cc_start: 0.6281 (m-80) cc_final: 0.5846 (m-10) REVERT: C 36 VAL cc_start: 0.7220 (t) cc_final: 0.7006 (t) REVERT: C 141 LEU cc_start: 0.2740 (OUTLIER) cc_final: 0.2486 (pp) REVERT: C 215 ASP cc_start: 0.4124 (OUTLIER) cc_final: 0.3282 (t0) REVERT: C 238 PHE cc_start: 0.4958 (OUTLIER) cc_final: 0.4460 (p90) REVERT: C 341 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 377 PHE cc_start: 0.3858 (OUTLIER) cc_final: 0.3070 (m-80) REVERT: C 394 ASN cc_start: 0.7373 (p0) cc_final: 0.6994 (p0) REVERT: C 396 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: C 461 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.5618 (tp) REVERT: C 481 ASN cc_start: 0.4051 (OUTLIER) cc_final: 0.2983 (p0) REVERT: C 492 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 524 VAL cc_start: 0.5270 (OUTLIER) cc_final: 0.5001 (t) REVERT: C 537 LYS cc_start: 0.3266 (OUTLIER) cc_final: 0.2737 (tmtt) outliers start: 510 outliers final: 70 residues processed: 1196 average time/residue: 0.2126 time to fit residues: 400.1605 Evaluate side-chains 471 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 371 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 206 GLU Chi-restraints excluded: chain L residue 209 LYS Chi-restraints excluded: chain c residue 61 LYS Chi-restraints excluded: chain c residue 66 LEU Chi-restraints excluded: chain c residue 86 SER Chi-restraints excluded: chain c residue 122 LYS Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 206 GLU Chi-restraints excluded: chain c residue 209 LYS Chi-restraints excluded: chain c residue 230 ARG Chi-restraints excluded: chain d residue 22 GLN Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 90 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain d residue 121 ARG Chi-restraints excluded: chain d residue 122 ARG Chi-restraints excluded: chain d residue 216 SER Chi-restraints excluded: chain f residue 61 LYS Chi-restraints excluded: chain f residue 66 LEU Chi-restraints excluded: chain f residue 141 ASP Chi-restraints excluded: chain g residue 22 GLN Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 133 GLN Chi-restraints excluded: chain g residue 148 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 370 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 762 GLN A 824 ASN A 907 ASN A 928 ASN A 954 GLN A 965 GLN A1005 GLN A1036 GLN H 227 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 46 GLN ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 GLN d 71 ASN d 84 GLN d 192 HIS ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 GLN g 71 ASN g 76 ASN g 84 GLN B 165 ASN B 188 ASN B 207 HIS B 370 ASN B 409 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 657 ASN B 709 ASN B 710 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN B1134 ASN C 115 GLN C 125 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 331 ASN C 409 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 657 ASN C 762 GLN C 928 ASN C 965 GLN C1054 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.112759 restraints weight = 119576.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.106062 restraints weight = 138075.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.104192 restraints weight = 114925.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.103247 restraints weight = 99664.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.103484 restraints weight = 84970.456| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34099 Z= 0.187 Angle : 0.809 13.546 46425 Z= 0.423 Chirality : 0.050 0.300 5244 Planarity : 0.007 0.147 5989 Dihedral : 8.586 68.651 4794 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.74 % Favored : 93.07 % Rotamer: Outliers : 4.56 % Allowed : 15.54 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.12), residues: 4226 helix: 0.34 (0.20), residues: 677 sheet: -1.05 (0.15), residues: 1173 loop : -2.18 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 121 TYR 0.039 0.002 TYR L 110 PHE 0.026 0.002 PHE A 135 TRP 0.032 0.003 TRP c 51 HIS 0.009 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00424 (34047) covalent geometry : angle 0.80553 (46323) SS BOND : bond 0.00761 ( 51) SS BOND : angle 1.86323 ( 102) hydrogen bonds : bond 0.05135 ( 1212) hydrogen bonds : angle 6.82267 ( 3456) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 409 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.7341 (mpt180) cc_final: 0.6425 (tmm160) REVERT: A 529 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6431 (ptmm) REVERT: H 51 TYR cc_start: 0.3950 (OUTLIER) cc_final: 0.3666 (m-80) REVERT: H 100 MET cc_start: 0.3421 (ptm) cc_final: 0.3096 (ptp) REVERT: H 101 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8040 (mm-30) REVERT: H 124 GLN cc_start: 0.5552 (tp40) cc_final: 0.5249 (tp-100) REVERT: L 23 MET cc_start: 0.1514 (mmm) cc_final: 0.0809 (tpp) REVERT: L 113 TYR cc_start: 0.2681 (OUTLIER) cc_final: 0.1957 (m-80) REVERT: L 186 ASP cc_start: 0.4935 (t70) cc_final: 0.4686 (t70) REVERT: c 209 LYS cc_start: 0.6313 (tptp) cc_final: 0.5158 (tmmt) REVERT: f 68 TYR cc_start: 0.8833 (p90) cc_final: 0.8278 (p90) REVERT: f 69 ASP cc_start: 0.8775 (m-30) cc_final: 0.8567 (m-30) REVERT: f 89 GLU cc_start: 0.8094 (tp30) cc_final: 0.7805 (tp30) REVERT: f 156 ASN cc_start: 0.2952 (t0) cc_final: 0.2541 (t0) REVERT: f 186 ASP cc_start: 0.5870 (t0) cc_final: 0.5608 (t70) REVERT: g 51 TYR cc_start: 0.4744 (OUTLIER) cc_final: 0.3275 (m-80) REVERT: g 54 HIS cc_start: 0.6616 (t-170) cc_final: 0.5980 (t70) REVERT: g 102 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7143 (tp) REVERT: g 108 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6232 (pm20) REVERT: g 109 ASP cc_start: 0.6934 (m-30) cc_final: 0.6458 (t70) REVERT: g 113 TYR cc_start: 0.7496 (m-80) cc_final: 0.7194 (m-80) REVERT: g 128 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 117 LEU cc_start: 0.9010 (tp) cc_final: 0.8771 (mt) REVERT: B 133 PHE cc_start: 0.6172 (m-10) cc_final: 0.5565 (m-10) REVERT: B 191 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7607 (mp0) REVERT: B 215 ASP cc_start: -0.0733 (OUTLIER) cc_final: -0.1121 (t0) REVERT: B 296 LEU cc_start: 0.8557 (tt) cc_final: 0.8000 (tt) REVERT: B 309 GLU cc_start: 0.6960 (mp0) cc_final: 0.6612 (mp0) REVERT: B 508 TYR cc_start: 0.7277 (m-80) cc_final: 0.7059 (m-10) REVERT: B 540 ASN cc_start: 0.2012 (OUTLIER) cc_final: 0.0879 (t0) REVERT: B 707 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8110 (p90) REVERT: B 823 PHE cc_start: 0.6418 (m-80) cc_final: 0.6213 (m-80) REVERT: C 91 TYR cc_start: 0.5888 (t80) cc_final: 0.5325 (t80) REVERT: C 141 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2654 (pp) REVERT: C 201 PHE cc_start: 0.6715 (t80) cc_final: 0.6334 (t80) REVERT: C 203 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.8012 (tt) REVERT: C 215 ASP cc_start: 0.3998 (OUTLIER) cc_final: 0.3289 (t70) REVERT: C 266 TYR cc_start: 0.5203 (m-80) cc_final: 0.4957 (m-80) REVERT: C 341 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8713 (p) REVERT: C 377 PHE cc_start: 0.4399 (OUTLIER) cc_final: 0.3809 (m-80) REVERT: C 396 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: C 408 ARG cc_start: 0.8307 (tmm160) cc_final: 0.7937 (ttp80) REVERT: C 429 PHE cc_start: 0.7849 (t80) cc_final: 0.7604 (t80) REVERT: C 452 LEU cc_start: 0.8853 (mp) cc_final: 0.8573 (mp) REVERT: C 481 ASN cc_start: 0.4660 (OUTLIER) cc_final: 0.3663 (p0) REVERT: C 492 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8026 (mt) REVERT: C 495 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5874 (t80) REVERT: C 606 ASN cc_start: 0.7697 (p0) cc_final: 0.7444 (p0) REVERT: C 692 ILE cc_start: 0.7629 (mt) cc_final: 0.7054 (mm) REVERT: C 1005 GLN cc_start: 0.8559 (tp40) cc_final: 0.8088 (tp-100) outliers start: 170 outliers final: 87 residues processed: 549 average time/residue: 0.1919 time to fit residues: 172.6088 Evaluate side-chains 411 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 305 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 205 TYR Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 186 ASP Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain d residue 198 LEU Chi-restraints excluded: chain f residue 86 SER Chi-restraints excluded: chain f residue 122 LYS Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 102 LEU Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 315 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 320 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 370 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 388 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 762 GLN A1005 GLN H 62 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN L 208 HIS c 46 GLN c 56 GLN ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 157 ASN d 192 HIS ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 824 ASN B 969 ASN C 122 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 331 ASN C 394 ASN C 414 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 751 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.135714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.108887 restraints weight = 118210.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.101885 restraints weight = 139972.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100107 restraints weight = 110615.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099258 restraints weight = 92617.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.099312 restraints weight = 96943.370| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 34099 Z= 0.168 Angle : 0.702 9.758 46425 Z= 0.366 Chirality : 0.047 0.245 5244 Planarity : 0.006 0.078 5989 Dihedral : 6.863 73.596 4670 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 4.56 % Allowed : 16.83 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 4226 helix: 0.85 (0.20), residues: 688 sheet: -0.61 (0.15), residues: 1169 loop : -2.02 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 983 TYR 0.040 0.002 TYR c 159 PHE 0.038 0.002 PHE A 157 TRP 0.054 0.002 TRP H 69 HIS 0.008 0.001 HIS L 208 Details of bonding type rmsd covalent geometry : bond 0.00388 (34047) covalent geometry : angle 0.69881 (46323) SS BOND : bond 0.00315 ( 51) SS BOND : angle 1.54306 ( 102) hydrogen bonds : bond 0.04529 ( 1212) hydrogen bonds : angle 6.17981 ( 3456) Misc. bond : bond 0.00265 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 345 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5514 (mtmm) REVERT: A 408 ARG cc_start: 0.7171 (mpt180) cc_final: 0.6375 (tmm160) REVERT: A 529 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.6917 (ptmm) REVERT: H 51 TYR cc_start: 0.3685 (OUTLIER) cc_final: 0.2569 (m-80) REVERT: H 100 MET cc_start: 0.3244 (ptm) cc_final: 0.2952 (ptm) REVERT: H 124 GLN cc_start: 0.5395 (tp40) cc_final: 0.5179 (tm-30) REVERT: L 23 MET cc_start: 0.1828 (mmm) cc_final: 0.1377 (tpp) REVERT: L 94 ILE cc_start: 0.4206 (OUTLIER) cc_final: 0.3952 (mm) REVERT: L 113 TYR cc_start: 0.3117 (OUTLIER) cc_final: 0.2214 (m-80) REVERT: L 166 GLN cc_start: 0.5359 (OUTLIER) cc_final: 0.4857 (mm-40) REVERT: c 209 LYS cc_start: 0.6077 (tptp) cc_final: 0.5151 (tmmt) REVERT: d 103 SER cc_start: 0.5784 (m) cc_final: 0.5453 (t) REVERT: f 68 TYR cc_start: 0.8783 (p90) cc_final: 0.8262 (p90) REVERT: f 102 PHE cc_start: 0.7571 (m-10) cc_final: 0.7156 (m-80) REVERT: f 156 ASN cc_start: 0.2846 (t0) cc_final: 0.2418 (t0) REVERT: g 51 TYR cc_start: 0.4547 (OUTLIER) cc_final: 0.2991 (m-80) REVERT: g 54 HIS cc_start: 0.6621 (t-170) cc_final: 0.5820 (t70) REVERT: g 109 ASP cc_start: 0.6933 (m-30) cc_final: 0.6698 (m-30) REVERT: g 128 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: B 215 ASP cc_start: -0.0668 (OUTLIER) cc_final: -0.1228 (t70) REVERT: B 274 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 309 GLU cc_start: 0.7494 (mp0) cc_final: 0.7258 (mp0) REVERT: B 442 ASP cc_start: 0.6481 (m-30) cc_final: 0.5777 (t70) REVERT: B 508 TYR cc_start: 0.7507 (m-80) cc_final: 0.7112 (m-80) REVERT: B 514 SER cc_start: 0.8579 (t) cc_final: 0.8293 (p) REVERT: B 540 ASN cc_start: 0.2345 (OUTLIER) cc_final: 0.1125 (t0) REVERT: B 707 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8204 (p90) REVERT: C 141 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3292 (pp) REVERT: C 214 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6879 (ptp-170) REVERT: C 215 ASP cc_start: 0.4398 (OUTLIER) cc_final: 0.3838 (t70) REVERT: C 347 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: C 377 PHE cc_start: 0.4916 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: C 408 ARG cc_start: 0.8446 (tmm160) cc_final: 0.8095 (ttp80) REVERT: C 429 PHE cc_start: 0.8085 (t80) cc_final: 0.7814 (t80) REVERT: C 452 LEU cc_start: 0.8795 (mp) cc_final: 0.8498 (mp) REVERT: C 456 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 481 ASN cc_start: 0.4842 (OUTLIER) cc_final: 0.4000 (p0) REVERT: C 492 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7968 (mt) REVERT: C 606 ASN cc_start: 0.8334 (p0) cc_final: 0.8112 (p0) outliers start: 170 outliers final: 84 residues processed: 484 average time/residue: 0.1901 time to fit residues: 151.5847 Evaluate side-chains 384 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 281 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain c residue 51 TRP Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 230 ARG Chi-restraints excluded: chain g residue 29 GLU Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 128 PHE Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 286 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 205 optimal weight: 40.0000 chunk 101 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 762 GLN A 992 GLN A1005 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 HIS ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** f 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 119 GLN ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 787 GLN C 935 GLN C 992 GLN C1005 GLN C1011 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.134125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.106288 restraints weight = 117788.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.099720 restraints weight = 139054.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098045 restraints weight = 109012.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.097175 restraints weight = 96893.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097018 restraints weight = 101467.454| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34099 Z= 0.164 Angle : 0.668 10.090 46425 Z= 0.346 Chirality : 0.046 0.226 5244 Planarity : 0.005 0.074 5989 Dihedral : 6.207 78.250 4642 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.92 % Favored : 93.87 % Rotamer: Outliers : 4.37 % Allowed : 17.95 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4226 helix: 1.03 (0.20), residues: 689 sheet: -0.49 (0.15), residues: 1237 loop : -2.00 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG f 43 TYR 0.020 0.002 TYR L 110 PHE 0.029 0.002 PHE C 559 TRP 0.028 0.002 TRP H 69 HIS 0.006 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00382 (34047) covalent geometry : angle 0.66502 (46323) SS BOND : bond 0.00441 ( 51) SS BOND : angle 1.52742 ( 102) hydrogen bonds : bond 0.04254 ( 1212) hydrogen bonds : angle 5.90065 ( 3456) Misc. bond : bond 0.00275 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 311 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5422 (ptt) cc_final: 0.4943 (ptt) REVERT: A 529 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7091 (ptmm) REVERT: A 991 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8897 (p) REVERT: H 51 TYR cc_start: 0.3367 (OUTLIER) cc_final: 0.1878 (m-80) REVERT: H 53 MET cc_start: 0.6807 (mmp) cc_final: 0.6499 (ttt) REVERT: L 23 MET cc_start: 0.1968 (mmm) cc_final: 0.1445 (tpp) REVERT: L 27 PRO cc_start: 0.4875 (Cg_exo) cc_final: 0.4658 (Cg_endo) REVERT: L 69 ASP cc_start: 0.8138 (t0) cc_final: 0.6984 (p0) REVERT: L 113 TYR cc_start: 0.3198 (OUTLIER) cc_final: 0.2215 (m-80) REVERT: L 166 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4947 (mm-40) REVERT: c 43 ARG cc_start: 0.6814 (mmp80) cc_final: 0.5972 (tpp-160) REVERT: c 209 LYS cc_start: 0.5912 (tptp) cc_final: 0.5251 (tmmt) REVERT: d 53 MET cc_start: 0.1614 (tpp) cc_final: 0.0512 (tpt) REVERT: f 37 ARG cc_start: 0.5786 (tmt-80) cc_final: 0.5376 (ttp80) REVERT: f 54 TRP cc_start: 0.6447 (m100) cc_final: 0.6086 (m100) REVERT: f 68 TYR cc_start: 0.8673 (p90) cc_final: 0.8209 (p90) REVERT: f 69 ASP cc_start: 0.8728 (m-30) cc_final: 0.8378 (m-30) REVERT: f 102 PHE cc_start: 0.7509 (m-10) cc_final: 0.7053 (m-80) REVERT: g 48 PHE cc_start: 0.6456 (t80) cc_final: 0.6246 (t80) REVERT: g 51 TYR cc_start: 0.4771 (OUTLIER) cc_final: 0.3140 (m-80) REVERT: g 54 HIS cc_start: 0.6901 (t-170) cc_final: 0.6276 (t70) REVERT: g 71 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7796 (p0) REVERT: g 109 ASP cc_start: 0.6746 (m-30) cc_final: 0.6468 (m-30) REVERT: g 122 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7628 (mtp180) REVERT: g 123 LEU cc_start: 0.7802 (pp) cc_final: 0.7237 (pp) REVERT: B 92 PHE cc_start: 0.7817 (t80) cc_final: 0.7076 (t80) REVERT: B 133 PHE cc_start: 0.7227 (m-10) cc_final: 0.6832 (m-10) REVERT: B 215 ASP cc_start: -0.0632 (OUTLIER) cc_final: -0.1242 (t70) REVERT: B 442 ASP cc_start: 0.6465 (m-30) cc_final: 0.6242 (m-30) REVERT: B 514 SER cc_start: 0.8666 (t) cc_final: 0.8359 (p) REVERT: B 533 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5519 (pp) REVERT: B 540 ASN cc_start: 0.2410 (OUTLIER) cc_final: 0.1246 (t0) REVERT: B 707 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (p90) REVERT: C 91 TYR cc_start: 0.6267 (t80) cc_final: 0.5599 (t80) REVERT: C 104 TRP cc_start: 0.6432 (p90) cc_final: 0.5502 (p90) REVERT: C 191 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7453 (tt0) REVERT: C 215 ASP cc_start: 0.4522 (OUTLIER) cc_final: 0.3753 (t70) REVERT: C 338 PHE cc_start: 0.8112 (m-10) cc_final: 0.7902 (m-10) REVERT: C 377 PHE cc_start: 0.5025 (OUTLIER) cc_final: 0.4525 (m-80) REVERT: C 429 PHE cc_start: 0.8265 (t80) cc_final: 0.8013 (t80) REVERT: C 452 LEU cc_start: 0.8733 (mp) cc_final: 0.8421 (mp) REVERT: C 456 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7757 (t80) REVERT: C 481 ASN cc_start: 0.4996 (OUTLIER) cc_final: 0.4198 (p0) REVERT: C 492 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7910 (mt) REVERT: C 1017 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7794 (tm-30) outliers start: 163 outliers final: 98 residues processed: 448 average time/residue: 0.1943 time to fit residues: 142.8518 Evaluate side-chains 382 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 268 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain c residue 51 TRP Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 77 THR Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 86 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 96 SER Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 290 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 238 optimal weight: 0.0980 chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 208 HIS c 25 GLN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS f 22 GLN ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 239 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 751 ASN B 787 GLN C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.130362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091753 restraints weight = 109333.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088245 restraints weight = 70974.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088168 restraints weight = 68333.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088379 restraints weight = 64324.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088443 restraints weight = 59365.481| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34099 Z= 0.179 Angle : 0.665 12.711 46425 Z= 0.343 Chirality : 0.046 0.214 5244 Planarity : 0.005 0.075 5989 Dihedral : 5.921 83.070 4631 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.71 % Rotamer: Outliers : 4.42 % Allowed : 19.27 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 4226 helix: 1.26 (0.20), residues: 673 sheet: -0.46 (0.14), residues: 1282 loop : -1.95 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.021 0.002 TYR L 110 PHE 0.025 0.002 PHE C 559 TRP 0.037 0.002 TRP g 69 HIS 0.006 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00410 (34047) covalent geometry : angle 0.66260 (46323) SS BOND : bond 0.00491 ( 51) SS BOND : angle 1.46759 ( 102) hydrogen bonds : bond 0.04195 ( 1212) hydrogen bonds : angle 5.75780 ( 3456) Misc. bond : bond 0.00285 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 301 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5464 (ptt) cc_final: 0.5072 (ptt) REVERT: A 200 TYR cc_start: 0.7754 (m-10) cc_final: 0.7241 (m-80) REVERT: A 392 PHE cc_start: 0.5614 (m-10) cc_final: 0.5390 (m-10) REVERT: A 470 THR cc_start: -0.2397 (OUTLIER) cc_final: -0.2849 (p) REVERT: A 529 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7424 (ptmm) REVERT: A 546 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7617 (tt) REVERT: H 51 TYR cc_start: 0.2794 (OUTLIER) cc_final: 0.1531 (m-80) REVERT: L 23 MET cc_start: 0.2179 (mmm) cc_final: 0.1590 (tpp) REVERT: L 27 PRO cc_start: 0.4771 (Cg_exo) cc_final: 0.4560 (Cg_endo) REVERT: L 69 ASP cc_start: 0.8394 (t0) cc_final: 0.7362 (p0) REVERT: L 113 TYR cc_start: 0.2698 (OUTLIER) cc_final: 0.2083 (m-80) REVERT: L 166 GLN cc_start: 0.5555 (OUTLIER) cc_final: 0.5205 (mm-40) REVERT: L 230 ARG cc_start: 0.2301 (OUTLIER) cc_final: 0.1791 (mtp85) REVERT: c 206 GLU cc_start: 0.3657 (OUTLIER) cc_final: 0.3365 (mm-30) REVERT: c 209 LYS cc_start: 0.5632 (tptp) cc_final: 0.5138 (tmmt) REVERT: d 53 MET cc_start: 0.2666 (tpp) cc_final: 0.1509 (tpt) REVERT: d 101 GLU cc_start: 0.6160 (mp0) cc_final: 0.5947 (mm-30) REVERT: d 103 SER cc_start: 0.5924 (m) cc_final: 0.5702 (t) REVERT: f 68 TYR cc_start: 0.8734 (p90) cc_final: 0.8446 (p90) REVERT: f 69 ASP cc_start: 0.8885 (m-30) cc_final: 0.8622 (m-30) REVERT: f 102 PHE cc_start: 0.7465 (m-10) cc_final: 0.7156 (m-80) REVERT: f 105 TYR cc_start: 0.8039 (m-80) cc_final: 0.7822 (m-80) REVERT: f 113 TYR cc_start: 0.3167 (OUTLIER) cc_final: 0.2246 (m-80) REVERT: f 206 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4548 (tp30) REVERT: g 48 PHE cc_start: 0.6767 (t80) cc_final: 0.6438 (t80) REVERT: g 51 TYR cc_start: 0.4643 (OUTLIER) cc_final: 0.2999 (m-80) REVERT: g 54 HIS cc_start: 0.6907 (t-170) cc_final: 0.6640 (t-170) REVERT: g 71 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.7735 (p0) REVERT: g 76 ASN cc_start: 0.7976 (m-40) cc_final: 0.7566 (m-40) REVERT: g 91 ARG cc_start: 0.7878 (pmt-80) cc_final: 0.7492 (ttp80) REVERT: g 109 ASP cc_start: 0.6545 (m-30) cc_final: 0.6220 (m-30) REVERT: g 122 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7787 (mtp180) REVERT: g 123 LEU cc_start: 0.7965 (pp) cc_final: 0.7283 (pp) REVERT: B 92 PHE cc_start: 0.7917 (t80) cc_final: 0.7296 (t80) REVERT: B 101 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6944 (mm) REVERT: B 133 PHE cc_start: 0.7295 (m-10) cc_final: 0.6797 (m-10) REVERT: B 189 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8478 (tp) REVERT: B 215 ASP cc_start: -0.0536 (OUTLIER) cc_final: -0.0950 (t70) REVERT: B 442 ASP cc_start: 0.6762 (m-30) cc_final: 0.6398 (m-30) REVERT: B 514 SER cc_start: 0.8600 (t) cc_final: 0.8245 (p) REVERT: B 540 ASN cc_start: 0.2420 (OUTLIER) cc_final: 0.1309 (t0) REVERT: B 574 ASP cc_start: 0.6444 (p0) cc_final: 0.5569 (m-30) REVERT: B 707 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8348 (p90) REVERT: C 91 TYR cc_start: 0.6531 (t80) cc_final: 0.6283 (t80) REVERT: C 104 TRP cc_start: 0.6785 (p90) cc_final: 0.6362 (p90) REVERT: C 191 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 213 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7835 (p) REVERT: C 215 ASP cc_start: 0.4588 (OUTLIER) cc_final: 0.3884 (t70) REVERT: C 377 PHE cc_start: 0.5109 (OUTLIER) cc_final: 0.4536 (m-80) REVERT: C 429 PHE cc_start: 0.8446 (t80) cc_final: 0.8116 (t80) REVERT: C 430 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 456 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 481 ASN cc_start: 0.5138 (OUTLIER) cc_final: 0.4365 (p0) REVERT: C 495 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.6089 (t80) REVERT: C 1017 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7990 (tm-30) outliers start: 165 outliers final: 104 residues processed: 444 average time/residue: 0.1888 time to fit residues: 138.5064 Evaluate side-chains 388 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 260 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 126 LYS Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 51 TRP Chi-restraints excluded: chain c residue 206 GLU Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 206 GLU Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 135 THR Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 219 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 707 TYR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 221 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 165 optimal weight: 0.3980 chunk 240 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1005 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 GLN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN C 613 GLN C1005 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.129217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097535 restraints weight = 108410.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.091717 restraints weight = 107084.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088591 restraints weight = 94282.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.087966 restraints weight = 93159.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088265 restraints weight = 77402.120| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34099 Z= 0.185 Angle : 0.669 12.299 46425 Z= 0.344 Chirality : 0.046 0.218 5244 Planarity : 0.005 0.074 5989 Dihedral : 5.801 86.126 4625 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.18 % Favored : 93.66 % Rotamer: Outliers : 4.66 % Allowed : 19.45 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4226 helix: 1.29 (0.20), residues: 669 sheet: -0.51 (0.15), residues: 1285 loop : -1.88 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 102 TYR 0.031 0.002 TYR d 99 PHE 0.030 0.002 PHE C 135 TRP 0.037 0.002 TRP g 69 HIS 0.009 0.001 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00432 (34047) covalent geometry : angle 0.66552 (46323) SS BOND : bond 0.00365 ( 51) SS BOND : angle 1.61210 ( 102) hydrogen bonds : bond 0.04280 ( 1212) hydrogen bonds : angle 5.63864 ( 3456) Misc. bond : bond 0.00368 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 296 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7730 (m-10) cc_final: 0.7330 (m-80) REVERT: A 229 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 470 THR cc_start: -0.2856 (OUTLIER) cc_final: -0.3308 (p) REVERT: A 529 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7728 (mmtm) REVERT: A 546 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7641 (tt) REVERT: H 51 TYR cc_start: 0.2763 (OUTLIER) cc_final: 0.1104 (m-80) REVERT: L 23 MET cc_start: 0.2058 (mmm) cc_final: 0.1565 (tpp) REVERT: L 27 PRO cc_start: 0.4671 (Cg_exo) cc_final: 0.4453 (Cg_endo) REVERT: L 113 TYR cc_start: 0.3667 (OUTLIER) cc_final: 0.2599 (m-80) REVERT: L 161 ARG cc_start: 0.7818 (mmt180) cc_final: 0.7572 (mmt90) REVERT: L 230 ARG cc_start: 0.2110 (OUTLIER) cc_final: 0.1496 (mtp85) REVERT: c 206 GLU cc_start: 0.3862 (OUTLIER) cc_final: 0.3601 (mm-30) REVERT: c 209 LYS cc_start: 0.5647 (tptp) cc_final: 0.5179 (tmmt) REVERT: d 53 MET cc_start: 0.1992 (tpp) cc_final: 0.1143 (tpt) REVERT: d 103 SER cc_start: 0.5706 (m) cc_final: 0.5418 (t) REVERT: f 54 TRP cc_start: 0.6406 (m100) cc_final: 0.5963 (m100) REVERT: f 68 TYR cc_start: 0.8629 (p90) cc_final: 0.8267 (p90) REVERT: f 69 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8426 (m-30) REVERT: f 105 TYR cc_start: 0.7687 (m-80) cc_final: 0.7468 (m-80) REVERT: f 113 TYR cc_start: 0.3202 (OUTLIER) cc_final: 0.2601 (m-80) REVERT: g 48 PHE cc_start: 0.6359 (t80) cc_final: 0.6065 (t80) REVERT: g 51 TYR cc_start: 0.4850 (OUTLIER) cc_final: 0.3141 (m-80) REVERT: g 71 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7747 (p0) REVERT: g 76 ASN cc_start: 0.7806 (m-40) cc_final: 0.7351 (m-40) REVERT: g 109 ASP cc_start: 0.6705 (m-30) cc_final: 0.6428 (m-30) REVERT: g 122 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7674 (mtp180) REVERT: g 123 LEU cc_start: 0.7632 (pp) cc_final: 0.7046 (pp) REVERT: B 92 PHE cc_start: 0.7781 (t80) cc_final: 0.7265 (t80) REVERT: B 133 PHE cc_start: 0.7175 (m-10) cc_final: 0.6814 (m-10) REVERT: B 215 ASP cc_start: -0.0125 (OUTLIER) cc_final: -0.0692 (t70) REVERT: B 442 ASP cc_start: 0.6316 (m-30) cc_final: 0.5949 (m-30) REVERT: B 514 SER cc_start: 0.8717 (t) cc_final: 0.8391 (p) REVERT: B 540 ASN cc_start: 0.3622 (OUTLIER) cc_final: 0.2111 (t0) REVERT: B 574 ASP cc_start: 0.6696 (p0) cc_final: 0.5901 (m-30) REVERT: B 770 ILE cc_start: 0.9174 (pt) cc_final: 0.8648 (mt) REVERT: C 213 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 215 ASP cc_start: 0.4692 (OUTLIER) cc_final: 0.4126 (t70) REVERT: C 377 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: C 408 ARG cc_start: 0.8614 (tmm160) cc_final: 0.8251 (ttp80) REVERT: C 429 PHE cc_start: 0.8620 (t80) cc_final: 0.8388 (t80) REVERT: C 430 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8702 (t) REVERT: C 456 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7866 (t80) REVERT: C 481 ASN cc_start: 0.5240 (OUTLIER) cc_final: 0.4322 (p0) REVERT: C 495 TYR cc_start: 0.5844 (t80) cc_final: 0.5636 (t80) REVERT: C 1017 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7763 (tm-30) outliers start: 174 outliers final: 114 residues processed: 443 average time/residue: 0.1839 time to fit residues: 135.6446 Evaluate side-chains 393 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 259 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 51 TRP Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 206 GLU Chi-restraints excluded: chain c residue 210 VAL Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 69 ASP Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 222 SER Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 71 ASN Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 409 optimal weight: 1.9990 chunk 413 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 266 optimal weight: 9.9990 chunk 269 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 99 optimal weight: 30.0000 chunk 402 optimal weight: 0.6980 chunk 342 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 957 GLN C 613 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.130116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096266 restraints weight = 108703.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.094723 restraints weight = 104310.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.094755 restraints weight = 73063.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094260 restraints weight = 53495.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.094372 restraints weight = 56618.666| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34099 Z= 0.124 Angle : 0.633 13.586 46425 Z= 0.322 Chirality : 0.045 0.242 5244 Planarity : 0.005 0.073 5989 Dihedral : 5.586 86.920 4624 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 3.91 % Allowed : 20.74 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4226 helix: 1.58 (0.21), residues: 670 sheet: -0.47 (0.15), residues: 1274 loop : -1.76 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.021 0.001 TYR A 453 PHE 0.031 0.001 PHE C 135 TRP 0.033 0.002 TRP g 69 HIS 0.009 0.001 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00285 (34047) covalent geometry : angle 0.63062 (46323) SS BOND : bond 0.00296 ( 51) SS BOND : angle 1.41423 ( 102) hydrogen bonds : bond 0.03858 ( 1212) hydrogen bonds : angle 5.43614 ( 3456) Misc. bond : bond 0.00252 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 281 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7536 (m-10) cc_final: 0.7232 (m-80) REVERT: A 229 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (pp) REVERT: A 546 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7631 (tt) REVERT: H 51 TYR cc_start: 0.3075 (OUTLIER) cc_final: 0.1327 (m-80) REVERT: L 23 MET cc_start: 0.1734 (mmm) cc_final: 0.1481 (tpp) REVERT: L 27 PRO cc_start: 0.4300 (Cg_exo) cc_final: 0.4089 (Cg_endo) REVERT: L 69 ASP cc_start: 0.7693 (t0) cc_final: 0.6781 (p0) REVERT: L 113 TYR cc_start: 0.4088 (OUTLIER) cc_final: 0.2917 (m-80) REVERT: L 166 GLN cc_start: 0.5331 (OUTLIER) cc_final: 0.4744 (mm-40) REVERT: L 230 ARG cc_start: 0.1958 (OUTLIER) cc_final: 0.1301 (mtp85) REVERT: c 206 GLU cc_start: 0.4416 (OUTLIER) cc_final: 0.4070 (mm-30) REVERT: c 209 LYS cc_start: 0.5687 (tptp) cc_final: 0.5239 (tmmt) REVERT: d 100 MET cc_start: 0.0735 (ptt) cc_final: 0.0119 (ptt) REVERT: d 103 SER cc_start: 0.4869 (m) cc_final: 0.4626 (t) REVERT: f 68 TYR cc_start: 0.8299 (p90) cc_final: 0.7883 (p90) REVERT: f 69 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: f 102 PHE cc_start: 0.7199 (m-10) cc_final: 0.6962 (m-80) REVERT: f 113 TYR cc_start: 0.3813 (OUTLIER) cc_final: 0.3040 (m-80) REVERT: g 51 TYR cc_start: 0.4965 (OUTLIER) cc_final: 0.3321 (m-80) REVERT: g 109 ASP cc_start: 0.6681 (m-30) cc_final: 0.6452 (m-30) REVERT: g 122 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7563 (mtt-85) REVERT: g 123 LEU cc_start: 0.7257 (pp) cc_final: 0.6843 (pp) REVERT: B 92 PHE cc_start: 0.7518 (t80) cc_final: 0.7044 (t80) REVERT: B 189 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 215 ASP cc_start: 0.0113 (OUTLIER) cc_final: -0.0466 (t0) REVERT: B 514 SER cc_start: 0.8732 (t) cc_final: 0.8464 (p) REVERT: B 574 ASP cc_start: 0.6622 (p0) cc_final: 0.5909 (m-30) REVERT: B 770 ILE cc_start: 0.9107 (pt) cc_final: 0.8652 (mt) REVERT: B 1050 MET cc_start: 0.7702 (mtp) cc_final: 0.7484 (mtp) REVERT: C 215 ASP cc_start: 0.4208 (OUTLIER) cc_final: 0.3952 (t70) REVERT: C 377 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.4936 (m-80) REVERT: C 429 PHE cc_start: 0.8517 (t80) cc_final: 0.8307 (t80) REVERT: C 481 ASN cc_start: 0.5207 (OUTLIER) cc_final: 0.4171 (p0) REVERT: C 1017 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8109 (tm-30) outliers start: 146 outliers final: 98 residues processed: 405 average time/residue: 0.1843 time to fit residues: 124.6931 Evaluate side-chains 368 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 255 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 206 GLU Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain d residue 125 PHE Chi-restraints excluded: chain f residue 69 ASP Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 392 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 204 optimal weight: 50.0000 chunk 373 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 304 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 396 optimal weight: 0.7980 chunk 134 optimal weight: 30.0000 chunk 138 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A1011 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 ASN d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 764 ASN B 954 GLN C 613 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.129118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090565 restraints weight = 108231.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087005 restraints weight = 69983.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.086712 restraints weight = 68791.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086903 restraints weight = 66522.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087002 restraints weight = 60718.008| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34099 Z= 0.154 Angle : 0.648 14.372 46425 Z= 0.331 Chirality : 0.045 0.208 5244 Planarity : 0.005 0.073 5989 Dihedral : 5.573 90.086 4620 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.34 % Favored : 93.52 % Rotamer: Outliers : 3.80 % Allowed : 21.20 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4226 helix: 1.39 (0.20), residues: 687 sheet: -0.41 (0.15), residues: 1242 loop : -1.73 (0.12), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG g 106 TYR 0.028 0.002 TYR L 192 PHE 0.042 0.002 PHE C 456 TRP 0.030 0.002 TRP g 69 HIS 0.011 0.001 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00361 (34047) covalent geometry : angle 0.64533 (46323) SS BOND : bond 0.00445 ( 51) SS BOND : angle 1.36869 ( 102) hydrogen bonds : bond 0.03980 ( 1212) hydrogen bonds : angle 5.43485 ( 3456) Misc. bond : bond 0.00286 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 267 time to evaluate : 1.036 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 200 TYR cc_start: 0.7829 (m-10) cc_final: 0.7471 (m-80) REVERT: A 229 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 546 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7658 (tt) REVERT: H 51 TYR cc_start: 0.2382 (OUTLIER) cc_final: 0.1146 (m-80) REVERT: L 23 MET cc_start: 0.2284 (mmm) cc_final: 0.1600 (tpp) REVERT: L 27 PRO cc_start: 0.4554 (Cg_exo) cc_final: 0.4350 (Cg_endo) REVERT: L 69 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7209 (p0) REVERT: L 113 TYR cc_start: 0.3180 (OUTLIER) cc_final: 0.2256 (m-80) REVERT: L 166 GLN cc_start: 0.5585 (OUTLIER) cc_final: 0.5235 (mm-40) REVERT: L 230 ARG cc_start: 0.2523 (OUTLIER) cc_final: 0.1990 (mtp85) REVERT: c 209 LYS cc_start: 0.5509 (tptp) cc_final: 0.5083 (pttm) REVERT: d 103 SER cc_start: 0.5924 (m) cc_final: 0.5718 (t) REVERT: f 54 TRP cc_start: 0.6707 (m100) cc_final: 0.6159 (m100) REVERT: f 68 TYR cc_start: 0.8646 (p90) cc_final: 0.8444 (p90) REVERT: f 113 TYR cc_start: 0.4034 (OUTLIER) cc_final: 0.3378 (m-80) REVERT: g 38 LYS cc_start: 0.8245 (tptt) cc_final: 0.8043 (tptt) REVERT: g 51 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.3032 (m-80) REVERT: g 109 ASP cc_start: 0.6362 (m-30) cc_final: 0.6029 (m-30) REVERT: g 122 ARG cc_start: 0.8245 (ttp-110) cc_final: 0.7840 (mtt-85) REVERT: g 123 LEU cc_start: 0.7959 (pp) cc_final: 0.7272 (pp) REVERT: B 92 PHE cc_start: 0.7917 (t80) cc_final: 0.7309 (t80) REVERT: B 189 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 215 ASP cc_start: 0.0186 (OUTLIER) cc_final: -0.0411 (t0) REVERT: B 514 SER cc_start: 0.8573 (t) cc_final: 0.8211 (p) REVERT: B 574 ASP cc_start: 0.6792 (p0) cc_final: 0.5905 (m-30) REVERT: B 770 ILE cc_start: 0.8943 (pt) cc_final: 0.8578 (mt) REVERT: C 106 PHE cc_start: 0.7263 (m-10) cc_final: 0.6937 (m-80) REVERT: C 201 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7595 (t80) REVERT: C 215 ASP cc_start: 0.4660 (OUTLIER) cc_final: 0.3963 (t70) REVERT: C 377 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4417 (m-80) REVERT: C 429 PHE cc_start: 0.8659 (t80) cc_final: 0.8444 (t80) REVERT: C 456 PHE cc_start: 0.8238 (t80) cc_final: 0.7852 (t80) REVERT: C 481 ASN cc_start: 0.5495 (OUTLIER) cc_final: 0.4794 (p0) REVERT: C 495 TYR cc_start: 0.5783 (t80) cc_final: 0.5468 (t80) outliers start: 142 outliers final: 100 residues processed: 388 average time/residue: 0.1796 time to fit residues: 116.9776 Evaluate side-chains 363 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 248 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 159 TYR Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 288 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 294 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 309 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 926 GLN A1005 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 954 GLN C 613 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.128002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088739 restraints weight = 107329.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085682 restraints weight = 72899.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.085525 restraints weight = 62319.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085844 restraints weight = 59998.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085837 restraints weight = 53076.543| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34099 Z= 0.180 Angle : 0.664 13.686 46425 Z= 0.340 Chirality : 0.046 0.230 5244 Planarity : 0.005 0.073 5989 Dihedral : 5.587 89.516 4617 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 3.97 % Allowed : 21.09 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4226 helix: 1.35 (0.20), residues: 687 sheet: -0.41 (0.15), residues: 1247 loop : -1.75 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 190 TYR 0.031 0.002 TYR C 612 PHE 0.038 0.002 PHE C 135 TRP 0.026 0.002 TRP L 115 HIS 0.010 0.001 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00424 (34047) covalent geometry : angle 0.66164 (46323) SS BOND : bond 0.00341 ( 51) SS BOND : angle 1.34382 ( 102) hydrogen bonds : bond 0.04140 ( 1212) hydrogen bonds : angle 5.48665 ( 3456) Misc. bond : bond 0.00289 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 259 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7916 (m-10) cc_final: 0.7563 (m-80) REVERT: A 229 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8206 (pp) REVERT: A 529 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8151 (mmtm) REVERT: A 546 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7717 (tt) REVERT: H 51 TYR cc_start: 0.2379 (OUTLIER) cc_final: 0.0979 (m-80) REVERT: H 76 ASN cc_start: 0.8068 (m110) cc_final: 0.6947 (t0) REVERT: L 23 MET cc_start: 0.2294 (mmm) cc_final: 0.1691 (tpp) REVERT: L 27 PRO cc_start: 0.4416 (Cg_exo) cc_final: 0.4214 (Cg_endo) REVERT: L 113 TYR cc_start: 0.3657 (OUTLIER) cc_final: 0.2749 (m-80) REVERT: L 166 GLN cc_start: 0.5555 (OUTLIER) cc_final: 0.5204 (mm-40) REVERT: L 230 ARG cc_start: 0.2638 (OUTLIER) cc_final: 0.2186 (mtp85) REVERT: c 209 LYS cc_start: 0.5493 (tptp) cc_final: 0.5063 (pttm) REVERT: d 103 SER cc_start: 0.5698 (m) cc_final: 0.5448 (t) REVERT: f 54 TRP cc_start: 0.6664 (m100) cc_final: 0.6078 (m100) REVERT: f 113 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.3546 (m-10) REVERT: g 38 LYS cc_start: 0.8242 (tptt) cc_final: 0.8007 (tptt) REVERT: g 51 TYR cc_start: 0.4976 (OUTLIER) cc_final: 0.3269 (m-80) REVERT: g 109 ASP cc_start: 0.6416 (m-30) cc_final: 0.6075 (m-30) REVERT: g 122 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7845 (mtt-85) REVERT: B 92 PHE cc_start: 0.7947 (t80) cc_final: 0.7349 (t80) REVERT: B 168 PHE cc_start: 0.8289 (t80) cc_final: 0.7930 (t80) REVERT: B 215 ASP cc_start: 0.0177 (OUTLIER) cc_final: -0.0483 (t0) REVERT: B 374 PHE cc_start: 0.7864 (m-10) cc_final: 0.7650 (m-80) REVERT: B 514 SER cc_start: 0.8567 (t) cc_final: 0.8211 (p) REVERT: B 574 ASP cc_start: 0.6975 (p0) cc_final: 0.6418 (t0) REVERT: B 770 ILE cc_start: 0.9175 (pt) cc_final: 0.8749 (mt) REVERT: B 954 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: C 201 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7668 (t80) REVERT: C 203 ILE cc_start: 0.8870 (pt) cc_final: 0.8500 (mp) REVERT: C 215 ASP cc_start: 0.4565 (OUTLIER) cc_final: 0.3949 (t70) REVERT: C 234 ASN cc_start: 0.5399 (OUTLIER) cc_final: 0.5157 (m110) REVERT: C 377 PHE cc_start: 0.5450 (OUTLIER) cc_final: 0.4675 (m-80) REVERT: C 395 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7936 (p) REVERT: C 456 PHE cc_start: 0.8261 (t80) cc_final: 0.7893 (t80) REVERT: C 481 ASN cc_start: 0.5449 (OUTLIER) cc_final: 0.4818 (p0) REVERT: C 495 TYR cc_start: 0.5625 (t80) cc_final: 0.5198 (t80) REVERT: C 1005 GLN cc_start: 0.8388 (tp40) cc_final: 0.8131 (tp-100) REVERT: C 1050 MET cc_start: 0.7961 (ptm) cc_final: 0.7723 (ptm) outliers start: 148 outliers final: 111 residues processed: 386 average time/residue: 0.1804 time to fit residues: 116.6151 Evaluate side-chains 379 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 251 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 62 GLN Chi-restraints excluded: chain d residue 107 SER Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain f residue 224 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 208 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 ASN ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 GLN d 62 GLN d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 954 GLN C 613 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.126596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085221 restraints weight = 108789.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083322 restraints weight = 67528.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083144 restraints weight = 55444.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083386 restraints weight = 61242.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083446 restraints weight = 51944.230| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34099 Z= 0.234 Angle : 0.708 15.349 46425 Z= 0.363 Chirality : 0.047 0.250 5244 Planarity : 0.005 0.073 5989 Dihedral : 5.695 88.658 4616 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 3.72 % Allowed : 21.30 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4226 helix: 1.24 (0.20), residues: 674 sheet: -0.44 (0.15), residues: 1264 loop : -1.79 (0.12), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 577 TYR 0.027 0.002 TYR C 380 PHE 0.032 0.002 PHE B 135 TRP 0.023 0.002 TRP A 353 HIS 0.010 0.002 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00548 (34047) covalent geometry : angle 0.70508 (46323) SS BOND : bond 0.00336 ( 51) SS BOND : angle 1.48917 ( 102) hydrogen bonds : bond 0.04457 ( 1212) hydrogen bonds : angle 5.60605 ( 3456) Misc. bond : bond 0.00318 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8452 Ramachandran restraints generated. 4226 Oldfield, 0 Emsley, 4226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 246 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7968 (m-10) cc_final: 0.7660 (m-80) REVERT: A 229 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8140 (pp) REVERT: A 529 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8257 (mmtm) REVERT: A 546 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7750 (tt) REVERT: H 51 TYR cc_start: 0.2054 (OUTLIER) cc_final: 0.0643 (m-80) REVERT: H 76 ASN cc_start: 0.8099 (m110) cc_final: 0.7028 (t0) REVERT: L 23 MET cc_start: 0.2348 (mmm) cc_final: 0.1728 (tpp) REVERT: L 113 TYR cc_start: 0.3703 (OUTLIER) cc_final: 0.2854 (m-80) REVERT: L 166 GLN cc_start: 0.5602 (OUTLIER) cc_final: 0.5293 (mm-40) REVERT: L 230 ARG cc_start: 0.2882 (OUTLIER) cc_final: 0.2440 (mtp85) REVERT: c 23 MET cc_start: 0.5394 (mmm) cc_final: 0.4467 (mmp) REVERT: c 209 LYS cc_start: 0.5461 (tptp) cc_final: 0.5093 (pttm) REVERT: f 54 TRP cc_start: 0.6740 (m100) cc_final: 0.6157 (m100) REVERT: f 113 TYR cc_start: 0.4212 (OUTLIER) cc_final: 0.3613 (m-80) REVERT: g 51 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.2964 (m-80) REVERT: g 109 ASP cc_start: 0.6391 (m-30) cc_final: 0.6071 (m-30) REVERT: g 122 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7877 (mtt-85) REVERT: B 92 PHE cc_start: 0.8014 (t80) cc_final: 0.7353 (t80) REVERT: B 102 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7210 (mmm-85) REVERT: B 168 PHE cc_start: 0.8296 (t80) cc_final: 0.7986 (t80) REVERT: B 374 PHE cc_start: 0.7973 (m-10) cc_final: 0.7678 (m-80) REVERT: B 408 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8380 (tmm160) REVERT: B 514 SER cc_start: 0.8540 (t) cc_final: 0.8148 (p) REVERT: B 770 ILE cc_start: 0.8841 (pt) cc_final: 0.8491 (mt) REVERT: B 954 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8514 (mt0) REVERT: B 955 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8411 (t0) REVERT: C 201 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7750 (t80) REVERT: C 215 ASP cc_start: 0.4415 (OUTLIER) cc_final: 0.3824 (t70) REVERT: C 377 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.4741 (m-80) REVERT: C 395 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7865 (p) REVERT: C 456 PHE cc_start: 0.8323 (t80) cc_final: 0.7955 (t80) REVERT: C 481 ASN cc_start: 0.5133 (OUTLIER) cc_final: 0.4502 (p0) REVERT: C 495 TYR cc_start: 0.5739 (t80) cc_final: 0.5339 (t80) REVERT: C 1005 GLN cc_start: 0.8471 (tp40) cc_final: 0.8234 (tp-100) REVERT: C 1017 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 1050 MET cc_start: 0.8009 (ptm) cc_final: 0.7803 (ptm) outliers start: 139 outliers final: 101 residues processed: 367 average time/residue: 0.1851 time to fit residues: 112.7813 Evaluate side-chains 354 residues out of total 3744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 237 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 211 THR Chi-restraints excluded: chain L residue 81 PHE Chi-restraints excluded: chain L residue 113 TYR Chi-restraints excluded: chain L residue 159 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 222 SER Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 230 ARG Chi-restraints excluded: chain c residue 215 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain f residue 107 CYS Chi-restraints excluded: chain f residue 113 TYR Chi-restraints excluded: chain f residue 136 ILE Chi-restraints excluded: chain f residue 182 VAL Chi-restraints excluded: chain g residue 51 TYR Chi-restraints excluded: chain g residue 108 GLU Chi-restraints excluded: chain g residue 156 SER Chi-restraints excluded: chain g residue 160 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 374 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 361 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 162 optimal weight: 0.0040 chunk 205 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 419 optimal weight: 0.8980 chunk 355 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 397 optimal weight: 0.0020 chunk 58 optimal weight: 3.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 992 GLN A1005 GLN ** H 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN d 192 HIS ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 954 GLN C 613 GLN C 926 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088399 restraints weight = 108143.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.087519 restraints weight = 70471.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.087080 restraints weight = 60494.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087360 restraints weight = 55715.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087359 restraints weight = 52870.830| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.7574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34099 Z= 0.118 Angle : 0.640 14.714 46425 Z= 0.327 Chirality : 0.045 0.218 5244 Planarity : 0.005 0.075 5989 Dihedral : 5.341 86.717 4616 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.27 % Rotamer: Outliers : 2.81 % Allowed : 22.43 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.02 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4226 helix: 1.53 (0.21), residues: 691 sheet: -0.29 (0.15), residues: 1268 loop : -1.66 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 983 TYR 0.021 0.001 TYR d 99 PHE 0.037 0.001 PHE C 135 TRP 0.031 0.002 TRP g 69 HIS 0.008 0.001 HIS g 54 Details of bonding type rmsd covalent geometry : bond 0.00263 (34047) covalent geometry : angle 0.63796 (46323) SS BOND : bond 0.00299 ( 51) SS BOND : angle 1.29550 ( 102) hydrogen bonds : bond 0.03728 ( 1212) hydrogen bonds : angle 5.30580 ( 3456) Misc. bond : bond 0.00315 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6878.33 seconds wall clock time: 119 minutes 7.21 seconds (7147.21 seconds total)