Starting phenix.real_space_refine on Wed Nov 19 23:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u76_8517/11_2025/5u76_8517.map" } resolution = 3.76 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= -0.176 sd= 0.627 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 220 5.16 5 C 18376 2.51 5 N 4748 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28364 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7091 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 46 Restraints were copied for chains: B, C, D Time building chain proxies: 7.39, per 1000 atoms: 0.26 Number of scatterers: 28364 At special positions: 0 Unit cell: (152.1, 152.1, 139.1, 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 220 16.00 O 5020 8.00 N 4748 7.00 C 18376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6752 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 54.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.672A pdb=" N ILE A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.587A pdb=" N LEU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR A 769 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 770' Processing helix chain 'A' and resid 785 through 795 Proline residue: A 793 - end of helix Processing helix chain 'A' and resid 800 through 804 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN A 899 " --> pdb=" O HIS A 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 900 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A 901 " --> pdb=" O SER A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 896 through 901' Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 917 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE A 933 " --> pdb=" O ALA A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 933' Processing helix chain 'A' and resid 934 through 939 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 957 No H-bonds generated for 'chain 'A' and resid 956 through 957' Processing helix chain 'A' and resid 958 through 959 No H-bonds generated for 'chain 'A' and resid 958 through 959' Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU A 969 " --> pdb=" O THR A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 991 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 992' Processing helix chain 'A' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A1007 " --> pdb=" O CYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER A1105 " --> pdb=" O GLN A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY A1132 " --> pdb=" O PRO A1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A1133 " --> pdb=" O THR A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1129 through 1133' Processing helix chain 'B' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.672A pdb=" N ILE B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Proline residue: B 322 - end of helix removed outlier: 3.587A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS B 565 " --> pdb=" O TYR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 618' Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 753 " --> pdb=" O PHE B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'B' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR B 769 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 765 through 770' Processing helix chain 'B' and resid 785 through 795 Proline residue: B 793 - end of helix Processing helix chain 'B' and resid 800 through 804 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 Processing helix chain 'B' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN B 899 " --> pdb=" O HIS B 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET B 900 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 901 " --> pdb=" O SER B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 896 through 901' Processing helix chain 'B' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE B 933 " --> pdb=" O ALA B 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 930 through 933' Processing helix chain 'B' and resid 934 through 939 Processing helix chain 'B' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 957 No H-bonds generated for 'chain 'B' and resid 956 through 957' Processing helix chain 'B' and resid 958 through 959 No H-bonds generated for 'chain 'B' and resid 958 through 959' Processing helix chain 'B' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU B 969 " --> pdb=" O THR B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU B 990 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP B 991 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 992 " --> pdb=" O ASP B 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 992' Processing helix chain 'B' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1004 " --> pdb=" O GLN B1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1007 " --> pdb=" O CYS B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY B1132 " --> pdb=" O PRO B1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B1133 " --> pdb=" O THR B1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1129 through 1133' Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix removed outlier: 3.672A pdb=" N ILE C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 230 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.587A pdb=" N LEU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 334 " --> pdb=" O TYR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN C 406 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 613 through 618' Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 753 " --> pdb=" O PHE C 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 753' Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR C 769 " --> pdb=" O ASP C 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 765 through 770' Processing helix chain 'C' and resid 785 through 795 Proline residue: C 793 - end of helix Processing helix chain 'C' and resid 800 through 804 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU C 842 " --> pdb=" O ASN C 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'C' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN C 899 " --> pdb=" O HIS C 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET C 900 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG C 901 " --> pdb=" O SER C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 896 through 901' Processing helix chain 'C' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU C 913 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE C 933 " --> pdb=" O ALA C 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 930 through 933' Processing helix chain 'C' and resid 934 through 939 Processing helix chain 'C' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 957 No H-bonds generated for 'chain 'C' and resid 956 through 957' Processing helix chain 'C' and resid 958 through 959 No H-bonds generated for 'chain 'C' and resid 958 through 959' Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU C 969 " --> pdb=" O THR C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU C 990 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP C 991 " --> pdb=" O ASP C 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 992' Processing helix chain 'C' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C1006 " --> pdb=" O LEU C1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C1007 " --> pdb=" O CYS C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER C1105 " --> pdb=" O GLN C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1127 Processing helix chain 'C' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY C1132 " --> pdb=" O PRO C1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C1133 " --> pdb=" O THR C1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1129 through 1133' Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.672A pdb=" N ILE D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU D 308 " --> pdb=" O TRP D 304 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.587A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN D 406 " --> pdb=" O PRO D 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS D 565 " --> pdb=" O TYR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 613 through 618' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG D 753 " --> pdb=" O PHE D 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 748 through 753' Processing helix chain 'D' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR D 769 " --> pdb=" O ASP D 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 765 through 770' Processing helix chain 'D' and resid 785 through 795 Proline residue: D 793 - end of helix Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 816 through 824 Processing helix chain 'D' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU D 842 " --> pdb=" O ASN D 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS D 845 " --> pdb=" O SER D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN D 899 " --> pdb=" O HIS D 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET D 900 " --> pdb=" O PRO D 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 901 " --> pdb=" O SER D 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 901' Processing helix chain 'D' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU D 913 " --> pdb=" O ASP D 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 916 " --> pdb=" O SER D 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 917 " --> pdb=" O LEU D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE D 933 " --> pdb=" O ALA D 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 930 through 933' Processing helix chain 'D' and resid 934 through 939 Processing helix chain 'D' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 957 No H-bonds generated for 'chain 'D' and resid 956 through 957' Processing helix chain 'D' and resid 958 through 959 No H-bonds generated for 'chain 'D' and resid 958 through 959' Processing helix chain 'D' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU D 969 " --> pdb=" O THR D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU D 990 " --> pdb=" O GLU D 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP D 991 " --> pdb=" O ASP D 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 992 " --> pdb=" O ASP D 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 987 through 992' Processing helix chain 'D' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS D1001 " --> pdb=" O ARG D 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D1004 " --> pdb=" O GLN D1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D1006 " --> pdb=" O LEU D1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D1007 " --> pdb=" O CYS D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1100 No H-bonds generated for 'chain 'D' and resid 1098 through 1100' Processing helix chain 'D' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER D1105 " --> pdb=" O GLN D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1127 Processing helix chain 'D' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY D1132 " --> pdb=" O PRO D1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D1133 " --> pdb=" O THR D1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1129 through 1133' Processing sheet with id=1, first strand: chain 'A' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL A 353 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 386 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 355 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 432 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN A 469 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 434 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 484 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 486 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE A 602 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 573 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=4, first strand: chain 'A' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU A 775 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 854 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 777 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR A 892 " --> pdb=" O PHE A 943 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'A' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP A1160 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A1012 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A1165 " --> pdb=" O PRO A1010 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL B 353 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU B 386 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 355 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 432 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN B 469 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 434 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 484 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 486 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 573 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 723 through 725 Processing sheet with id=10, first strand: chain 'B' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU B 775 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL B 854 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 777 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR B 892 " --> pdb=" O PHE B 943 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'B' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP B1160 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B1012 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B1165 " --> pdb=" O PRO B1010 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL C 353 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU C 386 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU C 355 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS C 432 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN C 469 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 434 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 484 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 486 " --> pdb=" O VAL C 468 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE C 602 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS C 573 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 723 through 725 Processing sheet with id=16, first strand: chain 'C' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU C 775 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL C 854 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 777 " --> pdb=" O VAL C 854 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR C 892 " --> pdb=" O PHE C 943 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'C' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP C1160 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C1012 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C1165 " --> pdb=" O PRO C1010 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL D 353 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU D 386 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU D 355 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS D 432 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN D 469 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 434 " --> pdb=" O GLN D 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 484 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 486 " --> pdb=" O VAL D 468 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE D 602 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS D 573 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 723 through 725 Processing sheet with id=22, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU D 775 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL D 854 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE D 777 " --> pdb=" O VAL D 854 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR D 892 " --> pdb=" O PHE D 943 " (cutoff:3.500A) No H-bonds generated for sheet with id=23 Processing sheet with id=24, first strand: chain 'D' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP D1160 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY D1012 " --> pdb=" O TYR D1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D1165 " --> pdb=" O PRO D1010 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3276 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: 5.88 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8808 1.34 - 1.46: 3656 1.46 - 1.58: 16228 1.58 - 1.69: 0 1.69 - 1.81: 332 Bond restraints: 29024 Sorted by residual: bond pdb=" CA PRO D1151 " pdb=" C PRO D1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO A1151 " pdb=" C PRO A1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO C1151 " pdb=" C PRO C1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO B1151 " pdb=" C PRO B1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 1.517 1.550 -0.033 9.30e-03 1.16e+04 1.24e+01 ... (remaining 29019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 34264 1.55 - 3.10: 4604 3.10 - 4.65: 376 4.65 - 6.20: 60 6.20 - 7.75: 16 Bond angle restraints: 39320 Sorted by residual: angle pdb=" N PRO C 208 " pdb=" CA PRO C 208 " pdb=" C PRO C 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO D 208 " pdb=" CA PRO D 208 " pdb=" C PRO D 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO A 208 " pdb=" CA PRO A 208 " pdb=" C PRO A 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N TYR B 960 " pdb=" CA TYR B 960 " pdb=" C TYR B 960 " ideal model delta sigma weight residual 111.75 117.69 -5.94 1.28e+00 6.10e-01 2.15e+01 ... (remaining 39315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 15604 15.03 - 30.07: 1348 30.07 - 45.10: 388 45.10 - 60.13: 80 60.13 - 75.17: 28 Dihedral angle restraints: 17448 sinusoidal: 7048 harmonic: 10400 Sorted by residual: dihedral pdb=" CA ARG B 438 " pdb=" C ARG B 438 " pdb=" N ASN B 439 " pdb=" CA ASN B 439 " ideal model delta harmonic sigma weight residual 180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG C 438 " pdb=" C ARG C 438 " pdb=" N ASN C 439 " pdb=" CA ASN C 439 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG A 438 " pdb=" C ARG A 438 " pdb=" N ASN A 439 " pdb=" CA ASN A 439 " ideal model delta harmonic sigma weight residual 180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 17445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2664 0.044 - 0.088: 1204 0.088 - 0.131: 388 0.131 - 0.175: 132 0.175 - 0.219: 56 Chirality restraints: 4444 Sorted by residual: chirality pdb=" CA VAL B 299 " pdb=" N VAL B 299 " pdb=" C VAL B 299 " pdb=" CB VAL B 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL C 299 " pdb=" N VAL C 299 " pdb=" C VAL C 299 " pdb=" CB VAL C 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL D 299 " pdb=" N VAL D 299 " pdb=" C VAL D 299 " pdb=" CB VAL D 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4441 not shown) Planarity restraints: 4924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 199 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO D 200 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 199 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 200 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 200 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.030 5.00e-02 4.00e+02 ... (remaining 4921 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 12 2.11 - 2.81: 4832 2.81 - 3.50: 38334 3.50 - 4.20: 62862 4.20 - 4.90: 114106 Nonbonded interactions: 220146 Sorted by model distance: nonbonded pdb=" OE2 GLU B 866 " pdb=" CB PRO C 388 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU C 866 " pdb=" CB PRO D 388 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU A 866 " pdb=" CB PRO B 388 " model vdw 1.410 3.440 nonbonded pdb=" CB PRO A 388 " pdb=" OE2 GLU D 866 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU A 866 " pdb=" CG PRO B 388 " model vdw 1.839 3.440 ... (remaining 220141 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.210 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 : 0.007 0.037 29024 Z= 0.528 Angle : 1.045 7.745 39320 Z= 0.705 Chirality : 0.060 0.219 4444 Planarity : 0.004 0.054 4924 Dihedral : 13.034 75.167 10696 Min Nonbonded Distance : 1.410 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.32 % Rotamer: Outliers : 0.51 % Allowed : 4.09 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.12), residues: 3456 helix: -2.17 (0.10), residues: 1504 sheet: -2.92 (0.23), residues: 316 loop : -2.56 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 993 TYR 0.015 0.001 TYR C 532 PHE 0.012 0.001 PHE B 931 TRP 0.010 0.001 TRP B 222 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00739 (29024) covalent geometry : angle 1.04487 (39320) hydrogen bonds : bond 0.28568 ( 1128) hydrogen bonds : angle 8.30679 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1060 time to evaluate : 1.165 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLN cc_start: 0.8324 (mt0) cc_final: 0.8075 (mm-40) REVERT: A 176 LEU cc_start: 0.7127 (mt) cc_final: 0.6446 (mt) REVERT: A 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7533 (p90) REVERT: A 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7778 (p90) REVERT: A 226 TYR cc_start: 0.7071 (t80) cc_final: 0.6667 (t80) REVERT: A 231 MET cc_start: 0.7544 (ttp) cc_final: 0.7307 (ttt) REVERT: A 309 LEU cc_start: 0.9416 (tp) cc_final: 0.9055 (tp) REVERT: A 326 GLU cc_start: 0.8478 (tt0) cc_final: 0.8077 (pp20) REVERT: A 358 SER cc_start: 0.8786 (t) cc_final: 0.8523 (p) REVERT: A 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8965 (t0) REVERT: A 371 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8141 (tp30) REVERT: A 375 HIS cc_start: 0.7388 (m90) cc_final: 0.6340 (m90) REVERT: A 382 TYR cc_start: 0.7872 (m-80) cc_final: 0.7587 (m-80) REVERT: A 383 VAL cc_start: 0.8033 (t) cc_final: 0.7780 (p) REVERT: A 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7987 (tt0) REVERT: A 470 ILE cc_start: 0.8140 (tp) cc_final: 0.7788 (tt) REVERT: A 489 GLU cc_start: 0.8376 (tt0) cc_final: 0.7928 (tp30) REVERT: A 538 ASN cc_start: 0.8429 (m110) cc_final: 0.8028 (m110) REVERT: A 572 VAL cc_start: 0.7606 (t) cc_final: 0.7402 (m) REVERT: A 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7514 (mmm) REVERT: A 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8944 (mt) REVERT: A 765 ASP cc_start: 0.7570 (m-30) cc_final: 0.6545 (p0) REVERT: A 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: A 903 MET cc_start: 0.8248 (tpt) cc_final: 0.7991 (tpp) REVERT: A 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: A 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8051 (m-80) REVERT: A 969 LEU cc_start: 0.9230 (mp) cc_final: 0.8847 (mp) REVERT: A 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7486 (mm) REVERT: A 1005 SER cc_start: 0.7690 (m) cc_final: 0.7421 (p) REVERT: A 1123 MET cc_start: 0.8326 (mtp) cc_final: 0.7893 (ttm) REVERT: A 1133 TYR cc_start: 0.8621 (t80) cc_final: 0.8390 (t80) REVERT: A 1137 ASN cc_start: 0.7578 (m-40) cc_final: 0.7371 (m110) REVERT: A 1157 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7576 (mp0) REVERT: A 1161 ILE cc_start: 0.7642 (mt) cc_final: 0.7405 (tp) REVERT: B 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: B 176 LEU cc_start: 0.7125 (mt) cc_final: 0.6444 (mt) REVERT: B 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7534 (p90) REVERT: B 218 PHE cc_start: 0.8084 (p90) cc_final: 0.7777 (p90) REVERT: B 226 TYR cc_start: 0.7071 (t80) cc_final: 0.6667 (t80) REVERT: B 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7307 (ttt) REVERT: B 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8946 (tp) REVERT: B 326 GLU cc_start: 0.8480 (tt0) cc_final: 0.8078 (pp20) REVERT: B 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: B 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8966 (t0) REVERT: B 371 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8141 (tp30) REVERT: B 375 HIS cc_start: 0.7387 (m90) cc_final: 0.6341 (m90) REVERT: B 382 TYR cc_start: 0.7871 (m-80) cc_final: 0.7587 (m-80) REVERT: B 383 VAL cc_start: 0.8033 (t) cc_final: 0.7780 (p) REVERT: B 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: B 470 ILE cc_start: 0.8139 (tp) cc_final: 0.7787 (tt) REVERT: B 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7929 (tp30) REVERT: B 538 ASN cc_start: 0.8428 (m110) cc_final: 0.8027 (m110) REVERT: B 572 VAL cc_start: 0.7607 (t) cc_final: 0.7402 (m) REVERT: B 595 MET cc_start: 0.8211 (mmp) cc_final: 0.7513 (mmm) REVERT: B 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8945 (mt) REVERT: B 765 ASP cc_start: 0.7568 (m-30) cc_final: 0.6544 (p0) REVERT: B 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: B 903 MET cc_start: 0.8247 (tpt) cc_final: 0.7992 (tpp) REVERT: B 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: B 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8051 (m-80) REVERT: B 969 LEU cc_start: 0.9230 (mp) cc_final: 0.8846 (mp) REVERT: B 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7485 (mm) REVERT: B 1005 SER cc_start: 0.7689 (m) cc_final: 0.7420 (p) REVERT: B 1123 MET cc_start: 0.8327 (mtp) cc_final: 0.7893 (ttm) REVERT: B 1133 TYR cc_start: 0.8620 (t80) cc_final: 0.8390 (t80) REVERT: B 1137 ASN cc_start: 0.7580 (m-40) cc_final: 0.7374 (m110) REVERT: B 1157 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7576 (mp0) REVERT: B 1161 ILE cc_start: 0.7644 (mt) cc_final: 0.7406 (tp) REVERT: C 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: C 176 LEU cc_start: 0.7125 (mt) cc_final: 0.6446 (mt) REVERT: C 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7534 (p90) REVERT: C 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7777 (p90) REVERT: C 226 TYR cc_start: 0.7070 (t80) cc_final: 0.6667 (t80) REVERT: C 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7306 (ttt) REVERT: C 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8946 (tp) REVERT: C 326 GLU cc_start: 0.8481 (tt0) cc_final: 0.8079 (pp20) REVERT: C 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: C 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8966 (t0) REVERT: C 371 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8141 (tp30) REVERT: C 375 HIS cc_start: 0.7387 (m90) cc_final: 0.6340 (m90) REVERT: C 382 TYR cc_start: 0.7871 (m-80) cc_final: 0.7588 (m-80) REVERT: C 383 VAL cc_start: 0.8036 (t) cc_final: 0.7781 (p) REVERT: C 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: C 470 ILE cc_start: 0.8140 (tp) cc_final: 0.7788 (tt) REVERT: C 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7928 (tp30) REVERT: C 538 ASN cc_start: 0.8427 (m110) cc_final: 0.8027 (m110) REVERT: C 572 VAL cc_start: 0.7607 (t) cc_final: 0.7402 (m) REVERT: C 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7513 (mmm) REVERT: C 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8944 (mt) REVERT: C 765 ASP cc_start: 0.7567 (m-30) cc_final: 0.6543 (p0) REVERT: C 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: C 903 MET cc_start: 0.8246 (tpt) cc_final: 0.7990 (tpp) REVERT: C 912 SER cc_start: 0.9069 (m) cc_final: 0.8798 (p) REVERT: C 953 TYR cc_start: 0.9171 (m-10) cc_final: 0.8051 (m-80) REVERT: C 969 LEU cc_start: 0.9231 (mp) cc_final: 0.8846 (mp) REVERT: C 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7486 (mm) REVERT: C 1005 SER cc_start: 0.7690 (m) cc_final: 0.7421 (p) REVERT: C 1123 MET cc_start: 0.8325 (mtp) cc_final: 0.7892 (ttm) REVERT: C 1133 TYR cc_start: 0.8622 (t80) cc_final: 0.8392 (t80) REVERT: C 1137 ASN cc_start: 0.7582 (m-40) cc_final: 0.7375 (m110) REVERT: C 1157 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7577 (mp0) REVERT: C 1161 ILE cc_start: 0.7644 (mt) cc_final: 0.7406 (tp) REVERT: D 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: D 176 LEU cc_start: 0.7126 (mt) cc_final: 0.6447 (mt) REVERT: D 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7533 (p90) REVERT: D 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7777 (p90) REVERT: D 226 TYR cc_start: 0.7070 (t80) cc_final: 0.6667 (t80) REVERT: D 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7306 (ttt) REVERT: D 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8945 (tp) REVERT: D 326 GLU cc_start: 0.8479 (tt0) cc_final: 0.8077 (pp20) REVERT: D 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: D 367 ASP cc_start: 0.9361 (m-30) cc_final: 0.8965 (t0) REVERT: D 371 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8140 (tp30) REVERT: D 375 HIS cc_start: 0.7386 (m90) cc_final: 0.6339 (m90) REVERT: D 382 TYR cc_start: 0.7870 (m-80) cc_final: 0.7587 (m-80) REVERT: D 383 VAL cc_start: 0.8035 (t) cc_final: 0.7781 (p) REVERT: D 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: D 470 ILE cc_start: 0.8139 (tp) cc_final: 0.7789 (tt) REVERT: D 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7929 (tp30) REVERT: D 538 ASN cc_start: 0.8429 (m110) cc_final: 0.8028 (m110) REVERT: D 572 VAL cc_start: 0.7605 (t) cc_final: 0.7401 (m) REVERT: D 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7513 (mmm) REVERT: D 743 LEU cc_start: 0.9206 (mt) cc_final: 0.8943 (mt) REVERT: D 765 ASP cc_start: 0.7569 (m-30) cc_final: 0.6546 (p0) REVERT: D 837 ASP cc_start: 0.9362 (t70) cc_final: 0.8881 (m-30) REVERT: D 903 MET cc_start: 0.8249 (tpt) cc_final: 0.7993 (tpp) REVERT: D 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: D 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8052 (m-80) REVERT: D 969 LEU cc_start: 0.9231 (mp) cc_final: 0.8846 (mp) REVERT: D 1002 LEU cc_start: 0.7937 (mt) cc_final: 0.7486 (mm) REVERT: D 1005 SER cc_start: 0.7689 (m) cc_final: 0.7420 (p) REVERT: D 1123 MET cc_start: 0.8326 (mtp) cc_final: 0.7893 (ttm) REVERT: D 1133 TYR cc_start: 0.8621 (t80) cc_final: 0.8391 (t80) REVERT: D 1137 ASN cc_start: 0.7580 (m-40) cc_final: 0.7373 (m110) REVERT: D 1157 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7577 (mp0) REVERT: D 1161 ILE cc_start: 0.7643 (mt) cc_final: 0.7405 (tp) outliers start: 16 outliers final: 0 residues processed: 1072 average time/residue: 0.1922 time to fit residues: 324.3688 Evaluate side-chains 682 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN B 904 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.084171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066240 restraints weight = 102896.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068628 restraints weight = 53691.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.070292 restraints weight = 33828.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.071561 restraints weight = 23973.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072305 restraints weight = 18334.515| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 29024 Z= 0.198 Angle : 0.784 10.909 39320 Z= 0.385 Chirality : 0.046 0.235 4444 Planarity : 0.005 0.058 4924 Dihedral : 4.957 17.798 3836 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.83 % Rotamer: Outliers : 2.71 % Allowed : 14.85 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3456 helix: -0.30 (0.12), residues: 1520 sheet: -1.75 (0.26), residues: 372 loop : -1.75 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 89 TYR 0.020 0.002 TYR D 798 PHE 0.029 0.002 PHE D 291 TRP 0.020 0.002 TRP B 455 HIS 0.006 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00448 (29024) covalent geometry : angle 0.78413 (39320) hydrogen bonds : bond 0.05442 ( 1128) hydrogen bonds : angle 5.34468 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 708 time to evaluate : 1.176 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: A 218 PHE cc_start: 0.7988 (p90) cc_final: 0.7536 (p90) REVERT: A 291 PHE cc_start: 0.7666 (m-80) cc_final: 0.7388 (m-80) REVERT: A 371 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8237 (tp30) REVERT: A 375 HIS cc_start: 0.8914 (m90) cc_final: 0.7096 (m90) REVERT: A 378 LEU cc_start: 0.8458 (mt) cc_final: 0.7788 (tt) REVERT: A 386 LEU cc_start: 0.9185 (tt) cc_final: 0.8643 (tt) REVERT: A 406 GLN cc_start: 0.8718 (tt0) cc_final: 0.8208 (pt0) REVERT: A 470 ILE cc_start: 0.9256 (tp) cc_final: 0.8961 (tt) REVERT: A 489 GLU cc_start: 0.9020 (tt0) cc_final: 0.8278 (tp30) REVERT: A 595 MET cc_start: 0.8388 (mmp) cc_final: 0.7972 (mmm) REVERT: A 743 LEU cc_start: 0.9613 (mt) cc_final: 0.9270 (mp) REVERT: A 795 ARG cc_start: 0.8489 (mmt180) cc_final: 0.7975 (mmt180) REVERT: A 832 MET cc_start: 0.7605 (mtt) cc_final: 0.7226 (mmm) REVERT: A 837 ASP cc_start: 0.9148 (t70) cc_final: 0.8870 (m-30) REVERT: A 881 MET cc_start: 0.9355 (mmm) cc_final: 0.8948 (mmm) REVERT: A 893 GLU cc_start: 0.8436 (pp20) cc_final: 0.7165 (tp30) REVERT: A 953 TYR cc_start: 0.9446 (m-10) cc_final: 0.8719 (m-80) REVERT: A 1005 SER cc_start: 0.8717 (m) cc_final: 0.8505 (p) REVERT: A 1137 ASN cc_start: 0.7658 (m-40) cc_final: 0.7111 (m-40) REVERT: A 1157 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8366 (mp0) REVERT: B 218 PHE cc_start: 0.7990 (p90) cc_final: 0.7537 (p90) REVERT: B 291 PHE cc_start: 0.7655 (m-80) cc_final: 0.7375 (m-80) REVERT: B 307 GLN cc_start: 0.9478 (mm-40) cc_final: 0.8865 (mp10) REVERT: B 371 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8238 (tp30) REVERT: B 375 HIS cc_start: 0.8924 (m90) cc_final: 0.7101 (m90) REVERT: B 378 LEU cc_start: 0.8460 (mt) cc_final: 0.7789 (tt) REVERT: B 386 LEU cc_start: 0.9185 (tt) cc_final: 0.8645 (tt) REVERT: B 406 GLN cc_start: 0.8717 (tt0) cc_final: 0.8206 (pt0) REVERT: B 470 ILE cc_start: 0.9257 (tp) cc_final: 0.8961 (tt) REVERT: B 489 GLU cc_start: 0.9026 (tt0) cc_final: 0.8283 (tp30) REVERT: B 595 MET cc_start: 0.8385 (mmp) cc_final: 0.7977 (mmm) REVERT: B 743 LEU cc_start: 0.9614 (mt) cc_final: 0.9270 (mp) REVERT: B 795 ARG cc_start: 0.8492 (mmt180) cc_final: 0.7984 (mmt180) REVERT: B 832 MET cc_start: 0.7590 (mtt) cc_final: 0.7219 (mmm) REVERT: B 837 ASP cc_start: 0.9144 (t70) cc_final: 0.8867 (m-30) REVERT: B 881 MET cc_start: 0.9355 (mmm) cc_final: 0.8948 (mmm) REVERT: B 893 GLU cc_start: 0.8439 (pp20) cc_final: 0.7161 (tp30) REVERT: B 953 TYR cc_start: 0.9448 (m-10) cc_final: 0.8720 (m-80) REVERT: B 1005 SER cc_start: 0.8713 (m) cc_final: 0.8502 (p) REVERT: B 1137 ASN cc_start: 0.7665 (m-40) cc_final: 0.7115 (m-40) REVERT: B 1157 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8366 (mp0) REVERT: C 218 PHE cc_start: 0.7992 (p90) cc_final: 0.7542 (p90) REVERT: C 291 PHE cc_start: 0.7661 (m-80) cc_final: 0.7383 (m-80) REVERT: C 307 GLN cc_start: 0.9477 (mm-40) cc_final: 0.8862 (mp10) REVERT: C 371 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8236 (tp30) REVERT: C 375 HIS cc_start: 0.8908 (m90) cc_final: 0.7094 (m90) REVERT: C 378 LEU cc_start: 0.8457 (mt) cc_final: 0.7789 (tt) REVERT: C 386 LEU cc_start: 0.9186 (tt) cc_final: 0.8643 (tt) REVERT: C 406 GLN cc_start: 0.8719 (tt0) cc_final: 0.8206 (pt0) REVERT: C 470 ILE cc_start: 0.9263 (tp) cc_final: 0.8968 (tt) REVERT: C 489 GLU cc_start: 0.9018 (tt0) cc_final: 0.8277 (tp30) REVERT: C 595 MET cc_start: 0.8373 (mmp) cc_final: 0.7970 (mmm) REVERT: C 743 LEU cc_start: 0.9613 (mt) cc_final: 0.9270 (mp) REVERT: C 795 ARG cc_start: 0.8490 (mmt180) cc_final: 0.7980 (mmt180) REVERT: C 832 MET cc_start: 0.7579 (mtt) cc_final: 0.7217 (mmm) REVERT: C 837 ASP cc_start: 0.9138 (t70) cc_final: 0.8868 (m-30) REVERT: C 881 MET cc_start: 0.9354 (mmm) cc_final: 0.8948 (mmm) REVERT: C 893 GLU cc_start: 0.8443 (pp20) cc_final: 0.7173 (tp30) REVERT: C 953 TYR cc_start: 0.9447 (m-10) cc_final: 0.8721 (m-80) REVERT: C 1005 SER cc_start: 0.8718 (m) cc_final: 0.8506 (p) REVERT: C 1137 ASN cc_start: 0.7653 (m-40) cc_final: 0.7106 (m-40) REVERT: C 1157 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8367 (mp0) REVERT: D 218 PHE cc_start: 0.7989 (p90) cc_final: 0.7532 (p90) REVERT: D 291 PHE cc_start: 0.7650 (m-80) cc_final: 0.7370 (m-80) REVERT: D 307 GLN cc_start: 0.9477 (mm-40) cc_final: 0.8864 (mp10) REVERT: D 371 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8235 (tp30) REVERT: D 375 HIS cc_start: 0.8910 (m90) cc_final: 0.7093 (m90) REVERT: D 378 LEU cc_start: 0.8452 (mt) cc_final: 0.7783 (tt) REVERT: D 386 LEU cc_start: 0.9184 (tt) cc_final: 0.8639 (tt) REVERT: D 406 GLN cc_start: 0.8718 (tt0) cc_final: 0.8205 (pt0) REVERT: D 470 ILE cc_start: 0.9259 (tp) cc_final: 0.8962 (tt) REVERT: D 489 GLU cc_start: 0.9023 (tt0) cc_final: 0.8280 (tp30) REVERT: D 595 MET cc_start: 0.8384 (mmp) cc_final: 0.7969 (mmm) REVERT: D 743 LEU cc_start: 0.9614 (mt) cc_final: 0.9270 (mp) REVERT: D 795 ARG cc_start: 0.8492 (mmt180) cc_final: 0.7981 (mmt180) REVERT: D 832 MET cc_start: 0.7590 (mtt) cc_final: 0.7220 (mmm) REVERT: D 837 ASP cc_start: 0.9142 (t70) cc_final: 0.8866 (m-30) REVERT: D 881 MET cc_start: 0.9353 (mmm) cc_final: 0.8948 (mmm) REVERT: D 943 PHE cc_start: 0.8840 (p90) cc_final: 0.8534 (p90) REVERT: D 953 TYR cc_start: 0.9448 (m-10) cc_final: 0.8721 (m-80) REVERT: D 1005 SER cc_start: 0.8714 (m) cc_final: 0.8503 (p) REVERT: D 1137 ASN cc_start: 0.7653 (m-40) cc_final: 0.7106 (m-40) REVERT: D 1157 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8368 (mp0) outliers start: 85 outliers final: 44 residues processed: 751 average time/residue: 0.1648 time to fit residues: 205.9225 Evaluate side-chains 602 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 558 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1008 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 204 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 270 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 69 optimal weight: 0.0570 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 HIS ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 HIS ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065903 restraints weight = 104824.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068271 restraints weight = 53505.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069927 restraints weight = 33265.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071122 restraints weight = 23353.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071974 restraints weight = 17905.031| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29024 Z= 0.155 Angle : 0.714 10.598 39320 Z= 0.342 Chirality : 0.044 0.186 4444 Planarity : 0.004 0.047 4924 Dihedral : 4.684 16.823 3836 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.54 % Favored : 95.34 % Rotamer: Outliers : 3.61 % Allowed : 17.82 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3456 helix: 0.17 (0.13), residues: 1528 sheet: -1.53 (0.26), residues: 440 loop : -1.31 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 89 TYR 0.018 0.002 TYR D1133 PHE 0.021 0.002 PHE D 905 TRP 0.011 0.001 TRP A 455 HIS 0.004 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00358 (29024) covalent geometry : angle 0.71421 (39320) hydrogen bonds : bond 0.04618 ( 1128) hydrogen bonds : angle 4.99091 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 613 time to evaluate : 1.092 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: symmetry clash REVERT: A 218 PHE cc_start: 0.7830 (p90) cc_final: 0.7334 (p90) REVERT: A 291 PHE cc_start: 0.7640 (m-80) cc_final: 0.7425 (m-80) REVERT: A 358 SER cc_start: 0.9254 (t) cc_final: 0.9010 (p) REVERT: A 371 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8166 (tp30) REVERT: A 375 HIS cc_start: 0.8760 (m90) cc_final: 0.7108 (m90) REVERT: A 378 LEU cc_start: 0.8403 (mt) cc_final: 0.7660 (tt) REVERT: A 386 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8954 (tt) REVERT: A 391 MET cc_start: 0.8093 (mmm) cc_final: 0.7414 (mmm) REVERT: A 406 GLN cc_start: 0.8508 (tt0) cc_final: 0.8171 (pt0) REVERT: A 595 MET cc_start: 0.8288 (mmp) cc_final: 0.7964 (mmm) REVERT: A 738 THR cc_start: 0.9388 (m) cc_final: 0.9062 (p) REVERT: A 743 LEU cc_start: 0.9562 (mt) cc_final: 0.9326 (mp) REVERT: A 823 ILE cc_start: 0.9365 (tt) cc_final: 0.9160 (pt) REVERT: A 832 MET cc_start: 0.7684 (mtt) cc_final: 0.7195 (mmm) REVERT: A 837 ASP cc_start: 0.9208 (t70) cc_final: 0.8863 (m-30) REVERT: A 844 GLN cc_start: 0.9584 (mt0) cc_final: 0.9311 (tt0) REVERT: A 881 MET cc_start: 0.9357 (mmm) cc_final: 0.9007 (mmm) REVERT: A 893 GLU cc_start: 0.8575 (pp20) cc_final: 0.7154 (tp30) REVERT: A 894 LEU cc_start: 0.9727 (mt) cc_final: 0.9336 (mt) REVERT: A 953 TYR cc_start: 0.9334 (m-10) cc_final: 0.8680 (m-80) REVERT: A 1123 MET cc_start: 0.8365 (ttm) cc_final: 0.8124 (ttm) REVERT: A 1137 ASN cc_start: 0.7584 (m-40) cc_final: 0.7155 (m-40) REVERT: A 1157 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8352 (mp0) REVERT: B 218 PHE cc_start: 0.7834 (p90) cc_final: 0.7337 (p90) REVERT: B 291 PHE cc_start: 0.7639 (m-80) cc_final: 0.7427 (m-80) REVERT: B 358 SER cc_start: 0.9258 (t) cc_final: 0.9012 (p) REVERT: B 371 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8172 (tp30) REVERT: B 375 HIS cc_start: 0.8771 (m90) cc_final: 0.7117 (m90) REVERT: B 378 LEU cc_start: 0.8401 (mt) cc_final: 0.7657 (tt) REVERT: B 386 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8960 (tt) REVERT: B 391 MET cc_start: 0.8098 (mmm) cc_final: 0.7411 (mmm) REVERT: B 406 GLN cc_start: 0.8507 (tt0) cc_final: 0.8167 (pt0) REVERT: B 595 MET cc_start: 0.8274 (mmp) cc_final: 0.7967 (mmm) REVERT: B 738 THR cc_start: 0.9390 (m) cc_final: 0.9063 (p) REVERT: B 743 LEU cc_start: 0.9558 (mt) cc_final: 0.9324 (mp) REVERT: B 823 ILE cc_start: 0.9364 (tt) cc_final: 0.9158 (pt) REVERT: B 832 MET cc_start: 0.7677 (mtt) cc_final: 0.7198 (mmm) REVERT: B 837 ASP cc_start: 0.9209 (t70) cc_final: 0.8864 (m-30) REVERT: B 844 GLN cc_start: 0.9585 (mt0) cc_final: 0.9312 (tt0) REVERT: B 881 MET cc_start: 0.9350 (mmm) cc_final: 0.8998 (mmm) REVERT: B 893 GLU cc_start: 0.8579 (pp20) cc_final: 0.7159 (tp30) REVERT: B 894 LEU cc_start: 0.9727 (mt) cc_final: 0.9339 (mt) REVERT: B 953 TYR cc_start: 0.9332 (m-10) cc_final: 0.8676 (m-80) REVERT: B 1123 MET cc_start: 0.8363 (ttm) cc_final: 0.8123 (ttm) REVERT: B 1137 ASN cc_start: 0.7611 (m-40) cc_final: 0.7181 (m-40) REVERT: B 1157 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8354 (mp0) REVERT: C 218 PHE cc_start: 0.7834 (p90) cc_final: 0.7339 (p90) REVERT: C 291 PHE cc_start: 0.7642 (m-80) cc_final: 0.7427 (m-80) REVERT: C 358 SER cc_start: 0.9261 (t) cc_final: 0.9015 (p) REVERT: C 371 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8170 (tp30) REVERT: C 375 HIS cc_start: 0.8754 (m90) cc_final: 0.7105 (m90) REVERT: C 378 LEU cc_start: 0.8395 (mt) cc_final: 0.7654 (tt) REVERT: C 386 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8959 (tt) REVERT: C 391 MET cc_start: 0.8099 (mmm) cc_final: 0.7412 (mmm) REVERT: C 406 GLN cc_start: 0.8506 (tt0) cc_final: 0.8167 (pt0) REVERT: C 595 MET cc_start: 0.8277 (mmp) cc_final: 0.7966 (mmm) REVERT: C 738 THR cc_start: 0.9389 (m) cc_final: 0.9063 (p) REVERT: C 743 LEU cc_start: 0.9563 (mt) cc_final: 0.9327 (mp) REVERT: C 823 ILE cc_start: 0.9362 (tt) cc_final: 0.9158 (pt) REVERT: C 832 MET cc_start: 0.7673 (mtt) cc_final: 0.7191 (mmm) REVERT: C 837 ASP cc_start: 0.9201 (t70) cc_final: 0.8860 (m-30) REVERT: C 844 GLN cc_start: 0.9585 (mt0) cc_final: 0.9311 (tt0) REVERT: C 869 MET cc_start: 0.8823 (ttm) cc_final: 0.8621 (ttp) REVERT: C 881 MET cc_start: 0.9353 (mmm) cc_final: 0.9001 (mmm) REVERT: C 893 GLU cc_start: 0.8576 (pp20) cc_final: 0.7156 (tp30) REVERT: C 894 LEU cc_start: 0.9727 (mt) cc_final: 0.9336 (mt) REVERT: C 953 TYR cc_start: 0.9332 (m-10) cc_final: 0.8675 (m-80) REVERT: C 1123 MET cc_start: 0.8360 (ttm) cc_final: 0.8120 (ttm) REVERT: C 1137 ASN cc_start: 0.7609 (m-40) cc_final: 0.7179 (m-40) REVERT: C 1157 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8350 (mp0) REVERT: D 218 PHE cc_start: 0.7831 (p90) cc_final: 0.7333 (p90) REVERT: D 291 PHE cc_start: 0.7628 (m-80) cc_final: 0.7416 (m-80) REVERT: D 371 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8164 (tp30) REVERT: D 375 HIS cc_start: 0.8750 (m90) cc_final: 0.7099 (m90) REVERT: D 378 LEU cc_start: 0.8396 (mt) cc_final: 0.7654 (tt) REVERT: D 386 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8957 (tt) REVERT: D 391 MET cc_start: 0.8093 (mmm) cc_final: 0.7416 (mmm) REVERT: D 406 GLN cc_start: 0.8506 (tt0) cc_final: 0.8167 (pt0) REVERT: D 595 MET cc_start: 0.8275 (mmp) cc_final: 0.7961 (mmm) REVERT: D 738 THR cc_start: 0.9391 (m) cc_final: 0.9066 (p) REVERT: D 743 LEU cc_start: 0.9565 (mt) cc_final: 0.9329 (mp) REVERT: D 823 ILE cc_start: 0.9363 (tt) cc_final: 0.9158 (pt) REVERT: D 832 MET cc_start: 0.7676 (mtt) cc_final: 0.7186 (mmm) REVERT: D 837 ASP cc_start: 0.9209 (t70) cc_final: 0.8864 (m-30) REVERT: D 844 GLN cc_start: 0.9583 (mt0) cc_final: 0.9309 (tt0) REVERT: D 881 MET cc_start: 0.9339 (mmm) cc_final: 0.8987 (mmm) REVERT: D 893 GLU cc_start: 0.8564 (pp20) cc_final: 0.7258 (tp30) REVERT: D 894 LEU cc_start: 0.9726 (mt) cc_final: 0.9376 (mt) REVERT: D 953 TYR cc_start: 0.9337 (m-10) cc_final: 0.8681 (m-80) REVERT: D 1123 MET cc_start: 0.8370 (ttm) cc_final: 0.8129 (ttm) REVERT: D 1137 ASN cc_start: 0.7576 (m-40) cc_final: 0.7147 (m-40) REVERT: D 1157 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8350 (mp0) outliers start: 113 outliers final: 65 residues processed: 694 average time/residue: 0.1648 time to fit residues: 191.6811 Evaluate side-chains 624 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 555 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1008 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 271 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS A 904 GLN A1149 ASN B 538 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS B 904 GLN B1149 ASN C 538 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 HIS C 904 GLN C1149 ASN D 538 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 HIS D 904 GLN D1149 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067334 restraints weight = 102749.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069761 restraints weight = 52901.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071439 restraints weight = 33110.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072629 restraints weight = 23333.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073451 restraints weight = 17915.125| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29024 Z= 0.126 Angle : 0.705 9.615 39320 Z= 0.331 Chirality : 0.044 0.207 4444 Planarity : 0.004 0.044 4924 Dihedral : 4.551 17.533 3836 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 3.07 % Allowed : 18.74 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3456 helix: 0.13 (0.13), residues: 1552 sheet: -1.26 (0.27), residues: 428 loop : -1.17 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 89 TYR 0.028 0.001 TYR B 285 PHE 0.017 0.001 PHE D 905 TRP 0.010 0.001 TRP B 455 HIS 0.004 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00295 (29024) covalent geometry : angle 0.70499 (39320) hydrogen bonds : bond 0.04099 ( 1128) hydrogen bonds : angle 4.80848 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 578 time to evaluate : 1.196 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 218 PHE cc_start: 0.7789 (p90) cc_final: 0.7302 (p90) REVERT: A 291 PHE cc_start: 0.7433 (m-80) cc_final: 0.7196 (m-80) REVERT: A 307 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8901 (mm110) REVERT: A 361 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8451 (mttt) REVERT: A 375 HIS cc_start: 0.8778 (m90) cc_final: 0.8329 (m90) REVERT: A 378 LEU cc_start: 0.8351 (mt) cc_final: 0.7602 (tt) REVERT: A 386 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 391 MET cc_start: 0.8137 (mmm) cc_final: 0.7855 (tpt) REVERT: A 406 GLN cc_start: 0.8628 (tt0) cc_final: 0.8391 (pt0) REVERT: A 471 LEU cc_start: 0.8667 (mt) cc_final: 0.8148 (mp) REVERT: A 595 MET cc_start: 0.8278 (mmp) cc_final: 0.7959 (mmm) REVERT: A 738 THR cc_start: 0.9379 (m) cc_final: 0.9076 (p) REVERT: A 743 LEU cc_start: 0.9588 (mt) cc_final: 0.9374 (mp) REVERT: A 837 ASP cc_start: 0.9205 (t70) cc_final: 0.8929 (m-30) REVERT: A 893 GLU cc_start: 0.8549 (pp20) cc_final: 0.7382 (tp30) REVERT: A 894 LEU cc_start: 0.9709 (mt) cc_final: 0.9369 (mm) REVERT: A 953 TYR cc_start: 0.9275 (m-10) cc_final: 0.8725 (m-80) REVERT: A 1123 MET cc_start: 0.8364 (ttm) cc_final: 0.8092 (ttm) REVERT: A 1137 ASN cc_start: 0.7495 (m-40) cc_final: 0.7116 (m-40) REVERT: A 1157 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8296 (mp0) REVERT: B 218 PHE cc_start: 0.7789 (p90) cc_final: 0.7302 (p90) REVERT: B 291 PHE cc_start: 0.7454 (m-80) cc_final: 0.7219 (m-80) REVERT: B 361 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8455 (mttt) REVERT: B 375 HIS cc_start: 0.8787 (m90) cc_final: 0.8336 (m90) REVERT: B 378 LEU cc_start: 0.8355 (mt) cc_final: 0.7605 (tt) REVERT: B 386 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8986 (tt) REVERT: B 406 GLN cc_start: 0.8625 (tt0) cc_final: 0.8386 (pt0) REVERT: B 471 LEU cc_start: 0.8669 (mt) cc_final: 0.8150 (mp) REVERT: B 595 MET cc_start: 0.8259 (mmp) cc_final: 0.7959 (mmm) REVERT: B 738 THR cc_start: 0.9379 (m) cc_final: 0.9075 (p) REVERT: B 743 LEU cc_start: 0.9586 (mt) cc_final: 0.9372 (mp) REVERT: B 837 ASP cc_start: 0.9206 (t70) cc_final: 0.8930 (m-30) REVERT: B 893 GLU cc_start: 0.8556 (pp20) cc_final: 0.7385 (tp30) REVERT: B 894 LEU cc_start: 0.9711 (mt) cc_final: 0.9372 (mm) REVERT: B 953 TYR cc_start: 0.9272 (m-10) cc_final: 0.8721 (m-80) REVERT: B 1123 MET cc_start: 0.8363 (ttm) cc_final: 0.8090 (ttm) REVERT: B 1157 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8300 (mp0) REVERT: C 218 PHE cc_start: 0.7791 (p90) cc_final: 0.7306 (p90) REVERT: C 291 PHE cc_start: 0.7458 (m-80) cc_final: 0.7223 (m-80) REVERT: C 361 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8458 (mttt) REVERT: C 375 HIS cc_start: 0.8771 (m90) cc_final: 0.8325 (m90) REVERT: C 378 LEU cc_start: 0.8352 (mt) cc_final: 0.7606 (tt) REVERT: C 386 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8981 (tt) REVERT: C 406 GLN cc_start: 0.8625 (tt0) cc_final: 0.8386 (pt0) REVERT: C 471 LEU cc_start: 0.8663 (mt) cc_final: 0.8146 (mp) REVERT: C 595 MET cc_start: 0.8261 (mmp) cc_final: 0.7961 (mmm) REVERT: C 738 THR cc_start: 0.9379 (m) cc_final: 0.9075 (p) REVERT: C 743 LEU cc_start: 0.9589 (mt) cc_final: 0.9376 (mp) REVERT: C 837 ASP cc_start: 0.9204 (t70) cc_final: 0.8929 (m-30) REVERT: C 893 GLU cc_start: 0.8546 (pp20) cc_final: 0.7382 (tp30) REVERT: C 894 LEU cc_start: 0.9709 (mt) cc_final: 0.9371 (mm) REVERT: C 953 TYR cc_start: 0.9273 (m-10) cc_final: 0.8721 (m-80) REVERT: C 1123 MET cc_start: 0.8365 (ttm) cc_final: 0.8092 (ttm) REVERT: C 1157 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8300 (mp0) REVERT: D 218 PHE cc_start: 0.7793 (p90) cc_final: 0.7306 (p90) REVERT: D 291 PHE cc_start: 0.7423 (m-80) cc_final: 0.7189 (m-80) REVERT: D 361 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8455 (mttt) REVERT: D 375 HIS cc_start: 0.8774 (m90) cc_final: 0.8323 (m90) REVERT: D 378 LEU cc_start: 0.8350 (mt) cc_final: 0.7599 (tt) REVERT: D 386 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8981 (tt) REVERT: D 391 MET cc_start: 0.8138 (mmm) cc_final: 0.7863 (tpt) REVERT: D 406 GLN cc_start: 0.8628 (tt0) cc_final: 0.8389 (pt0) REVERT: D 471 LEU cc_start: 0.8672 (mt) cc_final: 0.8092 (mp) REVERT: D 595 MET cc_start: 0.8258 (mmp) cc_final: 0.7956 (mmm) REVERT: D 738 THR cc_start: 0.9378 (m) cc_final: 0.9075 (p) REVERT: D 743 LEU cc_start: 0.9587 (mt) cc_final: 0.9375 (mp) REVERT: D 837 ASP cc_start: 0.9211 (t70) cc_final: 0.8932 (m-30) REVERT: D 893 GLU cc_start: 0.8527 (pp20) cc_final: 0.7378 (tp30) REVERT: D 894 LEU cc_start: 0.9711 (mt) cc_final: 0.9371 (mm) REVERT: D 953 TYR cc_start: 0.9278 (m-10) cc_final: 0.8726 (m-80) REVERT: D 1123 MET cc_start: 0.8365 (ttm) cc_final: 0.8092 (ttm) REVERT: D 1137 ASN cc_start: 0.7489 (m-40) cc_final: 0.7109 (m-40) REVERT: D 1157 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8297 (mp0) outliers start: 96 outliers final: 61 residues processed: 643 average time/residue: 0.1674 time to fit residues: 178.0064 Evaluate side-chains 603 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 538 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1008 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 341 optimal weight: 10.0000 chunk 5 optimal weight: 0.0270 chunk 333 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 183 optimal weight: 0.0770 chunk 138 optimal weight: 0.4980 chunk 194 optimal weight: 0.0980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.086274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068461 restraints weight = 102412.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070981 restraints weight = 51501.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072757 restraints weight = 32029.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073965 restraints weight = 22353.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074840 restraints weight = 17086.090| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29024 Z= 0.125 Angle : 0.731 12.544 39320 Z= 0.337 Chirality : 0.044 0.177 4444 Planarity : 0.004 0.042 4924 Dihedral : 4.513 16.320 3836 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.44 % Favored : 96.44 % Rotamer: Outliers : 3.61 % Allowed : 17.66 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3456 helix: 0.06 (0.13), residues: 1580 sheet: -1.04 (0.30), residues: 324 loop : -1.10 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.030 0.002 TYR C 285 PHE 0.026 0.002 PHE C 368 TRP 0.007 0.001 TRP C 528 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00288 (29024) covalent geometry : angle 0.73142 (39320) hydrogen bonds : bond 0.03894 ( 1128) hydrogen bonds : angle 4.67368 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 574 time to evaluate : 1.128 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: A 201 PHE cc_start: 0.9056 (m-80) cc_final: 0.8600 (t80) REVERT: A 218 PHE cc_start: 0.7639 (p90) cc_final: 0.7163 (p90) REVERT: A 285 TYR cc_start: 0.8757 (t80) cc_final: 0.8515 (t80) REVERT: A 291 PHE cc_start: 0.7634 (m-80) cc_final: 0.7380 (m-80) REVERT: A 307 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8829 (mm110) REVERT: A 361 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8455 (mttt) REVERT: A 375 HIS cc_start: 0.8702 (m90) cc_final: 0.8150 (m90) REVERT: A 378 LEU cc_start: 0.8255 (mt) cc_final: 0.7778 (pp) REVERT: A 386 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9021 (tt) REVERT: A 406 GLN cc_start: 0.8711 (tt0) cc_final: 0.8480 (pt0) REVERT: A 489 GLU cc_start: 0.8919 (tt0) cc_final: 0.8090 (tp30) REVERT: A 738 THR cc_start: 0.9392 (m) cc_final: 0.9177 (p) REVERT: A 781 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 832 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7625 (tpt) REVERT: A 837 ASP cc_start: 0.9155 (t70) cc_final: 0.8909 (m-30) REVERT: A 893 GLU cc_start: 0.8465 (pp20) cc_final: 0.7383 (tp30) REVERT: A 894 LEU cc_start: 0.9657 (mt) cc_final: 0.9286 (mm) REVERT: A 953 TYR cc_start: 0.9171 (m-10) cc_final: 0.8466 (m-80) REVERT: A 1123 MET cc_start: 0.8360 (ttm) cc_final: 0.8073 (ttm) REVERT: A 1157 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8285 (mp0) REVERT: B 201 PHE cc_start: 0.9054 (m-80) cc_final: 0.8600 (t80) REVERT: B 218 PHE cc_start: 0.7638 (p90) cc_final: 0.7160 (p90) REVERT: B 285 TYR cc_start: 0.8756 (t80) cc_final: 0.8533 (t80) REVERT: B 291 PHE cc_start: 0.7450 (m-80) cc_final: 0.7219 (m-80) REVERT: B 361 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8460 (mttt) REVERT: B 375 HIS cc_start: 0.8703 (m90) cc_final: 0.8153 (m90) REVERT: B 378 LEU cc_start: 0.8252 (mt) cc_final: 0.7777 (pp) REVERT: B 391 MET cc_start: 0.8672 (tpp) cc_final: 0.8012 (tpp) REVERT: B 406 GLN cc_start: 0.8713 (tt0) cc_final: 0.8481 (pt0) REVERT: B 489 GLU cc_start: 0.8919 (tt0) cc_final: 0.8088 (tp30) REVERT: B 738 THR cc_start: 0.9389 (m) cc_final: 0.9170 (p) REVERT: B 781 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: B 832 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7617 (tpt) REVERT: B 837 ASP cc_start: 0.9147 (t70) cc_final: 0.8907 (m-30) REVERT: B 893 GLU cc_start: 0.8469 (pp20) cc_final: 0.7384 (tp30) REVERT: B 894 LEU cc_start: 0.9659 (mt) cc_final: 0.9288 (mm) REVERT: B 953 TYR cc_start: 0.9168 (m-10) cc_final: 0.8464 (m-80) REVERT: B 1123 MET cc_start: 0.8364 (ttm) cc_final: 0.8076 (ttm) REVERT: B 1157 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8289 (mp0) REVERT: C 201 PHE cc_start: 0.9056 (m-80) cc_final: 0.8602 (t80) REVERT: C 218 PHE cc_start: 0.7643 (p90) cc_final: 0.7167 (p90) REVERT: C 291 PHE cc_start: 0.7664 (m-80) cc_final: 0.7410 (m-80) REVERT: C 361 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8459 (mttt) REVERT: C 375 HIS cc_start: 0.8710 (m90) cc_final: 0.8156 (m90) REVERT: C 378 LEU cc_start: 0.8254 (mt) cc_final: 0.7776 (pp) REVERT: C 391 MET cc_start: 0.8672 (tpp) cc_final: 0.8012 (tpp) REVERT: C 406 GLN cc_start: 0.8713 (tt0) cc_final: 0.8481 (pt0) REVERT: C 489 GLU cc_start: 0.8926 (tt0) cc_final: 0.8093 (tp30) REVERT: C 738 THR cc_start: 0.9386 (m) cc_final: 0.9169 (p) REVERT: C 781 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: C 832 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7621 (tpt) REVERT: C 837 ASP cc_start: 0.9157 (t70) cc_final: 0.8911 (m-30) REVERT: C 893 GLU cc_start: 0.8465 (pp20) cc_final: 0.7381 (tp30) REVERT: C 894 LEU cc_start: 0.9656 (mt) cc_final: 0.9285 (mm) REVERT: C 953 TYR cc_start: 0.9166 (m-10) cc_final: 0.8462 (m-80) REVERT: C 1123 MET cc_start: 0.8365 (ttm) cc_final: 0.8076 (ttm) REVERT: C 1157 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8286 (mp0) REVERT: D 201 PHE cc_start: 0.9058 (m-80) cc_final: 0.8603 (t80) REVERT: D 218 PHE cc_start: 0.7648 (p90) cc_final: 0.7173 (p90) REVERT: D 291 PHE cc_start: 0.7644 (m-80) cc_final: 0.7395 (m-80) REVERT: D 361 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8444 (mttt) REVERT: D 375 HIS cc_start: 0.8706 (m90) cc_final: 0.8151 (m90) REVERT: D 378 LEU cc_start: 0.8252 (mt) cc_final: 0.7772 (pp) REVERT: D 386 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9020 (tt) REVERT: D 406 GLN cc_start: 0.8713 (tt0) cc_final: 0.8481 (pt0) REVERT: D 471 LEU cc_start: 0.8799 (mt) cc_final: 0.8456 (mp) REVERT: D 738 THR cc_start: 0.9390 (m) cc_final: 0.9175 (p) REVERT: D 781 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: D 832 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7619 (tpt) REVERT: D 837 ASP cc_start: 0.9160 (t70) cc_final: 0.8913 (m-30) REVERT: D 893 GLU cc_start: 0.8445 (pp20) cc_final: 0.7325 (tp30) REVERT: D 894 LEU cc_start: 0.9665 (mt) cc_final: 0.9300 (mm) REVERT: D 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8470 (m-80) REVERT: D 1123 MET cc_start: 0.8364 (ttm) cc_final: 0.8075 (ttm) REVERT: D 1157 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8282 (mp0) outliers start: 113 outliers final: 62 residues processed: 652 average time/residue: 0.1627 time to fit residues: 176.6610 Evaluate side-chains 609 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 537 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 269 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 844 GLN A 852 ASN A 904 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 GLN B 852 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 GLN C 852 ASN D 475 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 GLN D 852 ASN D 904 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.085166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067797 restraints weight = 102922.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070256 restraints weight = 51562.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071993 restraints weight = 31964.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073213 restraints weight = 22299.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074075 restraints weight = 17001.275| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29024 Z= 0.134 Angle : 0.740 16.413 39320 Z= 0.340 Chirality : 0.045 0.227 4444 Planarity : 0.004 0.044 4924 Dihedral : 4.498 15.732 3836 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.51 % Allowed : 18.04 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3456 helix: 0.11 (0.13), residues: 1584 sheet: -0.76 (0.28), residues: 348 loop : -1.07 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.023 0.001 TYR C 285 PHE 0.024 0.001 PHE C 286 TRP 0.009 0.001 TRP D 304 HIS 0.004 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00319 (29024) covalent geometry : angle 0.74021 (39320) hydrogen bonds : bond 0.03743 ( 1128) hydrogen bonds : angle 4.67252 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 559 time to evaluate : 0.983 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: A 218 PHE cc_start: 0.7745 (p90) cc_final: 0.7273 (p90) REVERT: A 291 PHE cc_start: 0.7713 (m-80) cc_final: 0.7390 (m-80) REVERT: A 361 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8458 (mttt) REVERT: A 375 HIS cc_start: 0.8709 (m90) cc_final: 0.8292 (m90) REVERT: A 378 LEU cc_start: 0.8320 (mt) cc_final: 0.7862 (pp) REVERT: A 391 MET cc_start: 0.8574 (tpp) cc_final: 0.7849 (tpp) REVERT: A 406 GLN cc_start: 0.8687 (tt0) cc_final: 0.8343 (pt0) REVERT: A 531 MET cc_start: 0.9021 (mtt) cc_final: 0.8727 (tpt) REVERT: A 738 THR cc_start: 0.9372 (m) cc_final: 0.9155 (p) REVERT: A 765 ASP cc_start: 0.8504 (m-30) cc_final: 0.8296 (t70) REVERT: A 781 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 798 TYR cc_start: 0.9241 (p90) cc_final: 0.8148 (p90) REVERT: A 832 MET cc_start: 0.8248 (mmm) cc_final: 0.8024 (tpt) REVERT: A 837 ASP cc_start: 0.9171 (t70) cc_final: 0.8940 (m-30) REVERT: A 893 GLU cc_start: 0.8577 (pp20) cc_final: 0.7493 (tp30) REVERT: A 894 LEU cc_start: 0.9636 (mt) cc_final: 0.9274 (mm) REVERT: A 953 TYR cc_start: 0.9094 (m-10) cc_final: 0.8479 (m-80) REVERT: A 1123 MET cc_start: 0.8389 (ttm) cc_final: 0.8066 (ttm) REVERT: A 1157 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8291 (mp0) REVERT: B 218 PHE cc_start: 0.7743 (p90) cc_final: 0.7271 (p90) REVERT: B 272 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8473 (tp30) REVERT: B 291 PHE cc_start: 0.7549 (m-80) cc_final: 0.7251 (m-80) REVERT: B 361 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8460 (mttt) REVERT: B 375 HIS cc_start: 0.8705 (m90) cc_final: 0.8288 (m90) REVERT: B 378 LEU cc_start: 0.8320 (mt) cc_final: 0.7861 (pp) REVERT: B 391 MET cc_start: 0.8717 (tpp) cc_final: 0.8223 (tpp) REVERT: B 406 GLN cc_start: 0.8695 (tt0) cc_final: 0.8426 (pt0) REVERT: B 531 MET cc_start: 0.9021 (mtt) cc_final: 0.8727 (tpt) REVERT: B 738 THR cc_start: 0.9370 (m) cc_final: 0.9151 (p) REVERT: B 765 ASP cc_start: 0.8509 (m-30) cc_final: 0.8298 (t70) REVERT: B 781 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 798 TYR cc_start: 0.9239 (p90) cc_final: 0.8149 (p90) REVERT: B 832 MET cc_start: 0.8248 (mmm) cc_final: 0.8023 (tpt) REVERT: B 837 ASP cc_start: 0.9168 (t70) cc_final: 0.8938 (m-30) REVERT: B 893 GLU cc_start: 0.8587 (pp20) cc_final: 0.7496 (tp30) REVERT: B 894 LEU cc_start: 0.9636 (mt) cc_final: 0.9273 (mm) REVERT: B 953 TYR cc_start: 0.9090 (m-10) cc_final: 0.8477 (m-80) REVERT: B 1123 MET cc_start: 0.8389 (ttm) cc_final: 0.8068 (ttm) REVERT: B 1157 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8292 (mp0) REVERT: C 218 PHE cc_start: 0.7744 (p90) cc_final: 0.7271 (p90) REVERT: C 272 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8473 (tp30) REVERT: C 291 PHE cc_start: 0.7566 (m-80) cc_final: 0.7258 (m-80) REVERT: C 361 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8459 (mttt) REVERT: C 375 HIS cc_start: 0.8695 (m90) cc_final: 0.8282 (m90) REVERT: C 378 LEU cc_start: 0.8317 (mt) cc_final: 0.7864 (pp) REVERT: C 391 MET cc_start: 0.8715 (tpp) cc_final: 0.8221 (tpp) REVERT: C 406 GLN cc_start: 0.8697 (tt0) cc_final: 0.8427 (pt0) REVERT: C 531 MET cc_start: 0.9020 (mtt) cc_final: 0.8727 (tpt) REVERT: C 738 THR cc_start: 0.9370 (m) cc_final: 0.9152 (p) REVERT: C 765 ASP cc_start: 0.8506 (m-30) cc_final: 0.8299 (t70) REVERT: C 781 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: C 798 TYR cc_start: 0.9241 (p90) cc_final: 0.8146 (p90) REVERT: C 832 MET cc_start: 0.8246 (mmm) cc_final: 0.8019 (tpt) REVERT: C 837 ASP cc_start: 0.9166 (t70) cc_final: 0.8936 (m-30) REVERT: C 893 GLU cc_start: 0.8583 (pp20) cc_final: 0.7493 (tp30) REVERT: C 894 LEU cc_start: 0.9634 (mt) cc_final: 0.9268 (mm) REVERT: C 953 TYR cc_start: 0.9091 (m-10) cc_final: 0.8477 (m-80) REVERT: C 1123 MET cc_start: 0.8391 (ttm) cc_final: 0.8068 (ttm) REVERT: C 1157 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8291 (mp0) REVERT: D 218 PHE cc_start: 0.7756 (p90) cc_final: 0.7284 (p90) REVERT: D 272 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8470 (tp30) REVERT: D 291 PHE cc_start: 0.7499 (m-80) cc_final: 0.7211 (m-80) REVERT: D 361 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8459 (mttt) REVERT: D 375 HIS cc_start: 0.8697 (m90) cc_final: 0.8282 (m90) REVERT: D 378 LEU cc_start: 0.8322 (mt) cc_final: 0.7870 (pp) REVERT: D 406 GLN cc_start: 0.8692 (tt0) cc_final: 0.8348 (pt0) REVERT: D 531 MET cc_start: 0.9020 (mtt) cc_final: 0.8729 (tpt) REVERT: D 738 THR cc_start: 0.9372 (m) cc_final: 0.9156 (p) REVERT: D 765 ASP cc_start: 0.8508 (m-30) cc_final: 0.8295 (t70) REVERT: D 781 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: D 798 TYR cc_start: 0.9238 (p90) cc_final: 0.8145 (p90) REVERT: D 832 MET cc_start: 0.8272 (mmm) cc_final: 0.8038 (tpt) REVERT: D 837 ASP cc_start: 0.9171 (t70) cc_final: 0.8940 (m-30) REVERT: D 893 GLU cc_start: 0.8558 (pp20) cc_final: 0.7549 (tp30) REVERT: D 894 LEU cc_start: 0.9630 (mt) cc_final: 0.9228 (mm) REVERT: D 943 PHE cc_start: 0.8675 (p90) cc_final: 0.7784 (p90) REVERT: D 953 TYR cc_start: 0.9108 (m-10) cc_final: 0.8476 (m-80) REVERT: D 1123 MET cc_start: 0.8394 (ttm) cc_final: 0.8078 (ttm) REVERT: D 1157 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8287 (mp0) outliers start: 110 outliers final: 79 residues processed: 626 average time/residue: 0.1693 time to fit residues: 175.5303 Evaluate side-chains 599 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 516 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 852 ASN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 852 ASN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1009 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN D 904 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.084262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066720 restraints weight = 104498.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069167 restraints weight = 52533.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070866 restraints weight = 32565.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072044 restraints weight = 22859.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072917 restraints weight = 17540.589| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29024 Z= 0.155 Angle : 0.736 12.191 39320 Z= 0.341 Chirality : 0.045 0.233 4444 Planarity : 0.004 0.045 4924 Dihedral : 4.496 17.561 3836 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.19 % Allowed : 19.44 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3456 helix: 0.20 (0.13), residues: 1584 sheet: -0.79 (0.28), residues: 340 loop : -1.04 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 966 TYR 0.035 0.001 TYR C 285 PHE 0.022 0.002 PHE D 201 TRP 0.011 0.001 TRP B 304 HIS 0.005 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00358 (29024) covalent geometry : angle 0.73564 (39320) hydrogen bonds : bond 0.03762 ( 1128) hydrogen bonds : angle 4.67549 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 531 time to evaluate : 1.124 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 201 PHE cc_start: 0.8794 (m-80) cc_final: 0.8581 (t80) REVERT: A 218 PHE cc_start: 0.7745 (p90) cc_final: 0.7254 (p90) REVERT: A 291 PHE cc_start: 0.7568 (m-80) cc_final: 0.7317 (m-80) REVERT: A 307 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8987 (mm110) REVERT: A 375 HIS cc_start: 0.8674 (m90) cc_final: 0.8177 (m90) REVERT: A 378 LEU cc_start: 0.8348 (mt) cc_final: 0.8066 (pp) REVERT: A 382 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6588 (t80) REVERT: A 391 MET cc_start: 0.8757 (tpp) cc_final: 0.7979 (tpp) REVERT: A 397 ARG cc_start: 0.8288 (mmt90) cc_final: 0.8076 (tpt170) REVERT: A 406 GLN cc_start: 0.8680 (tt0) cc_final: 0.8441 (pt0) REVERT: A 426 MET cc_start: 0.9034 (mmm) cc_final: 0.8675 (mmm) REVERT: A 531 MET cc_start: 0.9052 (mtt) cc_final: 0.8778 (tpt) REVERT: A 545 MET cc_start: 0.7764 (mtm) cc_final: 0.7482 (ptp) REVERT: A 552 MET cc_start: 0.7907 (tpp) cc_final: 0.7388 (tpp) REVERT: A 595 MET cc_start: 0.8088 (mmp) cc_final: 0.7307 (mmp) REVERT: A 738 THR cc_start: 0.9354 (m) cc_final: 0.9147 (p) REVERT: A 765 ASP cc_start: 0.8613 (m-30) cc_final: 0.8322 (t70) REVERT: A 781 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 832 MET cc_start: 0.8447 (mmm) cc_final: 0.8163 (tpt) REVERT: A 837 ASP cc_start: 0.9178 (t70) cc_final: 0.8926 (m-30) REVERT: A 893 GLU cc_start: 0.8631 (pp20) cc_final: 0.7590 (tp30) REVERT: A 894 LEU cc_start: 0.9630 (mt) cc_final: 0.9159 (mm) REVERT: A 953 TYR cc_start: 0.9076 (m-10) cc_final: 0.8450 (m-80) REVERT: A 1123 MET cc_start: 0.8388 (ttm) cc_final: 0.8044 (ttm) REVERT: A 1157 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8331 (mp0) REVERT: B 201 PHE cc_start: 0.8779 (m-80) cc_final: 0.8511 (t80) REVERT: B 218 PHE cc_start: 0.7746 (p90) cc_final: 0.7255 (p90) REVERT: B 291 PHE cc_start: 0.7646 (m-80) cc_final: 0.7416 (m-80) REVERT: B 375 HIS cc_start: 0.8687 (m90) cc_final: 0.8185 (m90) REVERT: B 378 LEU cc_start: 0.8350 (mt) cc_final: 0.8066 (pp) REVERT: B 382 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6583 (t80) REVERT: B 391 MET cc_start: 0.8910 (tpp) cc_final: 0.8430 (tpp) REVERT: B 406 GLN cc_start: 0.8685 (tt0) cc_final: 0.8448 (pt0) REVERT: B 426 MET cc_start: 0.9029 (mmm) cc_final: 0.8706 (mmm) REVERT: B 531 MET cc_start: 0.9052 (mtt) cc_final: 0.8779 (tpt) REVERT: B 545 MET cc_start: 0.7770 (mtm) cc_final: 0.7483 (ptp) REVERT: B 552 MET cc_start: 0.7900 (tpp) cc_final: 0.7380 (tpp) REVERT: B 595 MET cc_start: 0.8089 (mmp) cc_final: 0.7312 (mmp) REVERT: B 738 THR cc_start: 0.9352 (m) cc_final: 0.9145 (p) REVERT: B 765 ASP cc_start: 0.8617 (m-30) cc_final: 0.8322 (t70) REVERT: B 781 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: B 832 MET cc_start: 0.8453 (mmm) cc_final: 0.8169 (tpt) REVERT: B 837 ASP cc_start: 0.9180 (t70) cc_final: 0.8925 (m-30) REVERT: B 893 GLU cc_start: 0.8639 (pp20) cc_final: 0.7593 (tp30) REVERT: B 894 LEU cc_start: 0.9633 (mt) cc_final: 0.9165 (mm) REVERT: B 953 TYR cc_start: 0.9081 (m-10) cc_final: 0.8455 (m-80) REVERT: B 1123 MET cc_start: 0.8399 (ttm) cc_final: 0.8048 (ttm) REVERT: B 1157 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8333 (mp0) REVERT: C 201 PHE cc_start: 0.8800 (m-80) cc_final: 0.8584 (t80) REVERT: C 218 PHE cc_start: 0.7745 (p90) cc_final: 0.7254 (p90) REVERT: C 291 PHE cc_start: 0.7508 (m-80) cc_final: 0.7264 (m-80) REVERT: C 375 HIS cc_start: 0.8676 (m90) cc_final: 0.8179 (m90) REVERT: C 378 LEU cc_start: 0.8346 (mt) cc_final: 0.8065 (pp) REVERT: C 382 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6583 (t80) REVERT: C 391 MET cc_start: 0.8907 (tpp) cc_final: 0.8427 (tpp) REVERT: C 406 GLN cc_start: 0.8683 (tt0) cc_final: 0.8448 (pt0) REVERT: C 426 MET cc_start: 0.9027 (mmm) cc_final: 0.8705 (mmm) REVERT: C 531 MET cc_start: 0.9053 (mtt) cc_final: 0.8780 (tpt) REVERT: C 545 MET cc_start: 0.7776 (mtm) cc_final: 0.7484 (ptp) REVERT: C 552 MET cc_start: 0.7913 (tpp) cc_final: 0.7395 (tpp) REVERT: C 595 MET cc_start: 0.8082 (mmp) cc_final: 0.7309 (mmp) REVERT: C 738 THR cc_start: 0.9351 (m) cc_final: 0.9144 (p) REVERT: C 765 ASP cc_start: 0.8620 (m-30) cc_final: 0.8316 (t70) REVERT: C 781 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: C 832 MET cc_start: 0.8450 (mmm) cc_final: 0.8165 (tpt) REVERT: C 837 ASP cc_start: 0.9184 (t70) cc_final: 0.8928 (m-30) REVERT: C 893 GLU cc_start: 0.8638 (pp20) cc_final: 0.7595 (tp30) REVERT: C 894 LEU cc_start: 0.9631 (mt) cc_final: 0.9165 (mm) REVERT: C 953 TYR cc_start: 0.9078 (m-10) cc_final: 0.8450 (m-80) REVERT: C 1123 MET cc_start: 0.8405 (ttm) cc_final: 0.8054 (ttm) REVERT: C 1157 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8334 (mp0) REVERT: D 201 PHE cc_start: 0.8782 (m-80) cc_final: 0.8512 (t80) REVERT: D 218 PHE cc_start: 0.7762 (p90) cc_final: 0.7269 (p90) REVERT: D 272 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8438 (tp30) REVERT: D 291 PHE cc_start: 0.7605 (m-80) cc_final: 0.7378 (m-80) REVERT: D 375 HIS cc_start: 0.8682 (m90) cc_final: 0.8181 (m90) REVERT: D 378 LEU cc_start: 0.8343 (mt) cc_final: 0.8059 (pp) REVERT: D 382 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6528 (t80) REVERT: D 406 GLN cc_start: 0.8683 (tt0) cc_final: 0.8444 (pt0) REVERT: D 426 MET cc_start: 0.9048 (mmm) cc_final: 0.8733 (mmm) REVERT: D 531 MET cc_start: 0.9053 (mtt) cc_final: 0.8780 (tpt) REVERT: D 545 MET cc_start: 0.7759 (mtm) cc_final: 0.7479 (ptp) REVERT: D 552 MET cc_start: 0.7913 (tpp) cc_final: 0.7395 (tpp) REVERT: D 595 MET cc_start: 0.8081 (mmp) cc_final: 0.7301 (mmp) REVERT: D 738 THR cc_start: 0.9353 (m) cc_final: 0.9143 (p) REVERT: D 765 ASP cc_start: 0.8618 (m-30) cc_final: 0.8317 (t70) REVERT: D 781 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: D 832 MET cc_start: 0.8441 (mmm) cc_final: 0.8157 (tpt) REVERT: D 837 ASP cc_start: 0.9189 (t70) cc_final: 0.8930 (m-30) REVERT: D 893 GLU cc_start: 0.8619 (pp20) cc_final: 0.7584 (tp30) REVERT: D 894 LEU cc_start: 0.9627 (mt) cc_final: 0.9241 (mm) REVERT: D 953 TYR cc_start: 0.9075 (m-10) cc_final: 0.8447 (m-80) REVERT: D 1123 MET cc_start: 0.8399 (ttm) cc_final: 0.8052 (ttm) REVERT: D 1157 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8331 (mp0) outliers start: 100 outliers final: 76 residues processed: 598 average time/residue: 0.1639 time to fit residues: 164.1247 Evaluate side-chains 585 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 501 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 382 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 382 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.1980 chunk 127 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 282 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN D 904 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066989 restraints weight = 105495.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069437 restraints weight = 54359.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.071125 restraints weight = 33816.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072276 restraints weight = 23803.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073145 restraints weight = 18336.905| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29024 Z= 0.140 Angle : 0.752 12.351 39320 Z= 0.346 Chirality : 0.045 0.240 4444 Planarity : 0.004 0.045 4924 Dihedral : 4.457 17.192 3836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.07 % Allowed : 21.01 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 3456 helix: 0.28 (0.13), residues: 1576 sheet: -0.76 (0.27), residues: 380 loop : -1.02 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 966 TYR 0.024 0.001 TYR A 285 PHE 0.023 0.001 PHE B 905 TRP 0.013 0.001 TRP D 304 HIS 0.005 0.001 HIS D1139 Details of bonding type rmsd covalent geometry : bond 0.00331 (29024) covalent geometry : angle 0.75153 (39320) hydrogen bonds : bond 0.03842 ( 1128) hydrogen bonds : angle 4.66459 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 508 time to evaluate : 1.199 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: A 218 PHE cc_start: 0.7824 (p90) cc_final: 0.7271 (p90) REVERT: A 291 PHE cc_start: 0.7608 (m-80) cc_final: 0.7384 (m-80) REVERT: A 310 VAL cc_start: 0.9297 (m) cc_final: 0.9070 (p) REVERT: A 311 VAL cc_start: 0.9525 (t) cc_final: 0.9256 (t) REVERT: A 346 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7713 (ttp-170) REVERT: A 361 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8380 (mttt) REVERT: A 375 HIS cc_start: 0.8803 (m90) cc_final: 0.8290 (m90) REVERT: A 382 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 391 MET cc_start: 0.8827 (tpp) cc_final: 0.8110 (tpp) REVERT: A 397 ARG cc_start: 0.8300 (mmt90) cc_final: 0.8086 (tpt170) REVERT: A 426 MET cc_start: 0.9129 (mmm) cc_final: 0.8780 (mmm) REVERT: A 471 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 531 MET cc_start: 0.9012 (mtt) cc_final: 0.8792 (tpt) REVERT: A 545 MET cc_start: 0.7800 (mtm) cc_final: 0.7538 (ptp) REVERT: A 552 MET cc_start: 0.7906 (tpp) cc_final: 0.7415 (tpp) REVERT: A 561 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.5624 (t80) REVERT: A 595 MET cc_start: 0.8144 (mmp) cc_final: 0.7580 (mmp) REVERT: A 738 THR cc_start: 0.9355 (m) cc_final: 0.9152 (p) REVERT: A 765 ASP cc_start: 0.8546 (m-30) cc_final: 0.8177 (t70) REVERT: A 781 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: A 832 MET cc_start: 0.8367 (mmm) cc_final: 0.8097 (tpt) REVERT: A 893 GLU cc_start: 0.8648 (pp20) cc_final: 0.7529 (tp30) REVERT: A 894 LEU cc_start: 0.9616 (mt) cc_final: 0.9231 (mm) REVERT: A 900 MET cc_start: 0.9368 (mmm) cc_final: 0.9009 (mmm) REVERT: A 953 TYR cc_start: 0.9047 (m-10) cc_final: 0.8464 (m-80) REVERT: A 1123 MET cc_start: 0.8425 (ttm) cc_final: 0.8032 (ttm) REVERT: A 1137 ASN cc_start: 0.7590 (m-40) cc_final: 0.7209 (m-40) REVERT: B 218 PHE cc_start: 0.7829 (p90) cc_final: 0.7275 (p90) REVERT: B 346 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7710 (ttp-170) REVERT: B 361 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8389 (mttt) REVERT: B 375 HIS cc_start: 0.8804 (m90) cc_final: 0.8291 (m90) REVERT: B 382 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6483 (t80) REVERT: B 391 MET cc_start: 0.8932 (tpp) cc_final: 0.8439 (tpp) REVERT: B 426 MET cc_start: 0.9115 (mmm) cc_final: 0.8772 (mmm) REVERT: B 471 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 531 MET cc_start: 0.9013 (mtt) cc_final: 0.8794 (tpt) REVERT: B 545 MET cc_start: 0.7785 (mtm) cc_final: 0.7540 (ptp) REVERT: B 552 MET cc_start: 0.7906 (tpp) cc_final: 0.7415 (tpp) REVERT: B 561 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.5627 (t80) REVERT: B 595 MET cc_start: 0.8137 (mmp) cc_final: 0.7578 (mmp) REVERT: B 738 THR cc_start: 0.9357 (m) cc_final: 0.9154 (p) REVERT: B 765 ASP cc_start: 0.8550 (m-30) cc_final: 0.8179 (t70) REVERT: B 781 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: B 832 MET cc_start: 0.8370 (mmm) cc_final: 0.8102 (tpt) REVERT: B 893 GLU cc_start: 0.8657 (pp20) cc_final: 0.7532 (tp30) REVERT: B 894 LEU cc_start: 0.9616 (mt) cc_final: 0.9230 (mm) REVERT: B 900 MET cc_start: 0.9368 (mmm) cc_final: 0.9011 (mmm) REVERT: B 953 TYR cc_start: 0.9056 (m-10) cc_final: 0.8471 (m-80) REVERT: B 1123 MET cc_start: 0.8423 (ttm) cc_final: 0.8029 (ttm) REVERT: C 218 PHE cc_start: 0.7832 (p90) cc_final: 0.7274 (p90) REVERT: C 285 TYR cc_start: 0.8450 (t80) cc_final: 0.8174 (t80) REVERT: C 346 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7711 (ttp-170) REVERT: C 361 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8389 (mttt) REVERT: C 375 HIS cc_start: 0.8793 (m90) cc_final: 0.8284 (m90) REVERT: C 382 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6486 (t80) REVERT: C 391 MET cc_start: 0.8930 (tpp) cc_final: 0.8438 (tpp) REVERT: C 426 MET cc_start: 0.9113 (mmm) cc_final: 0.8771 (mmm) REVERT: C 471 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7997 (mm) REVERT: C 531 MET cc_start: 0.9014 (mtt) cc_final: 0.8796 (tpt) REVERT: C 545 MET cc_start: 0.7818 (mtm) cc_final: 0.7547 (ptp) REVERT: C 552 MET cc_start: 0.7917 (tpp) cc_final: 0.7427 (tpp) REVERT: C 561 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5624 (t80) REVERT: C 595 MET cc_start: 0.8140 (mmp) cc_final: 0.7580 (mmp) REVERT: C 738 THR cc_start: 0.9353 (m) cc_final: 0.9150 (p) REVERT: C 765 ASP cc_start: 0.8549 (m-30) cc_final: 0.8173 (t70) REVERT: C 781 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: C 832 MET cc_start: 0.8364 (mmm) cc_final: 0.8096 (tpt) REVERT: C 893 GLU cc_start: 0.8651 (pp20) cc_final: 0.7535 (tp30) REVERT: C 894 LEU cc_start: 0.9621 (mt) cc_final: 0.9248 (mm) REVERT: C 900 MET cc_start: 0.9371 (mmm) cc_final: 0.9014 (mmm) REVERT: C 953 TYR cc_start: 0.9056 (m-10) cc_final: 0.8470 (m-80) REVERT: C 1123 MET cc_start: 0.8424 (ttm) cc_final: 0.8030 (ttm) REVERT: C 1137 ASN cc_start: 0.7629 (m-40) cc_final: 0.7243 (m-40) REVERT: D 218 PHE cc_start: 0.7853 (p90) cc_final: 0.7298 (p90) REVERT: D 272 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8539 (tp30) REVERT: D 346 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7709 (ttp-170) REVERT: D 361 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8392 (mttt) REVERT: D 375 HIS cc_start: 0.8798 (m90) cc_final: 0.8288 (m90) REVERT: D 382 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6381 (t80) REVERT: D 426 MET cc_start: 0.9116 (mmm) cc_final: 0.8780 (mmm) REVERT: D 531 MET cc_start: 0.9013 (mtt) cc_final: 0.8795 (tpt) REVERT: D 545 MET cc_start: 0.7803 (mtm) cc_final: 0.7544 (ptp) REVERT: D 552 MET cc_start: 0.7918 (tpp) cc_final: 0.7428 (tpp) REVERT: D 561 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5626 (t80) REVERT: D 595 MET cc_start: 0.8146 (mmp) cc_final: 0.7575 (mmp) REVERT: D 765 ASP cc_start: 0.8549 (m-30) cc_final: 0.8171 (t70) REVERT: D 781 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: D 832 MET cc_start: 0.8404 (mmm) cc_final: 0.8119 (tpt) REVERT: D 893 GLU cc_start: 0.8642 (pp20) cc_final: 0.7569 (tp30) REVERT: D 894 LEU cc_start: 0.9625 (mt) cc_final: 0.9231 (mm) REVERT: D 900 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9040 (mmm) REVERT: D 943 PHE cc_start: 0.8789 (p90) cc_final: 0.7668 (p90) REVERT: D 953 TYR cc_start: 0.9051 (m-10) cc_final: 0.8473 (m-80) REVERT: D 1123 MET cc_start: 0.8427 (ttm) cc_final: 0.8033 (ttm) outliers start: 96 outliers final: 76 residues processed: 577 average time/residue: 0.1630 time to fit residues: 158.5134 Evaluate side-chains 579 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 487 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 382 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 382 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 303 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 134 optimal weight: 0.0670 chunk 52 optimal weight: 0.0000 chunk 289 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 259 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 overall best weight: 1.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN B 499 ASN D 499 ASN D 904 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.084595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067260 restraints weight = 104150.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069738 restraints weight = 53217.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071400 restraints weight = 33077.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072574 restraints weight = 23418.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073427 restraints weight = 17937.310| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29024 Z= 0.132 Angle : 0.758 11.481 39320 Z= 0.349 Chirality : 0.045 0.226 4444 Planarity : 0.004 0.045 4924 Dihedral : 4.417 16.321 3836 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.22 % Allowed : 21.26 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3456 helix: 0.32 (0.13), residues: 1584 sheet: -0.69 (0.27), residues: 380 loop : -0.97 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 966 TYR 0.026 0.001 TYR A 285 PHE 0.039 0.002 PHE D 291 TRP 0.011 0.001 TRP A 304 HIS 0.004 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00310 (29024) covalent geometry : angle 0.75777 (39320) hydrogen bonds : bond 0.03681 ( 1128) hydrogen bonds : angle 4.68318 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 514 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8876 (m-80) cc_final: 0.8603 (t80) REVERT: A 218 PHE cc_start: 0.7842 (p90) cc_final: 0.7394 (p90) REVERT: A 303 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8628 (mt) REVERT: A 346 ARG cc_start: 0.8246 (ttm170) cc_final: 0.7765 (ttp-170) REVERT: A 361 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8477 (mttt) REVERT: A 375 HIS cc_start: 0.8784 (m90) cc_final: 0.8274 (m90) REVERT: A 382 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6524 (t80) REVERT: A 391 MET cc_start: 0.8841 (tpp) cc_final: 0.8108 (tpp) REVERT: A 426 MET cc_start: 0.9142 (mmm) cc_final: 0.8812 (mmm) REVERT: A 490 GLU cc_start: 0.8854 (tt0) cc_final: 0.8211 (tm-30) REVERT: A 552 MET cc_start: 0.7892 (tpp) cc_final: 0.7398 (tpp) REVERT: A 561 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 595 MET cc_start: 0.8117 (mmp) cc_final: 0.7576 (mmp) REVERT: A 765 ASP cc_start: 0.8573 (m-30) cc_final: 0.8177 (t70) REVERT: A 781 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 832 MET cc_start: 0.8364 (mmm) cc_final: 0.8091 (tpt) REVERT: A 893 GLU cc_start: 0.8635 (pp20) cc_final: 0.7545 (tp30) REVERT: A 894 LEU cc_start: 0.9626 (mt) cc_final: 0.9136 (mm) REVERT: A 900 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9045 (mmm) REVERT: A 953 TYR cc_start: 0.9054 (m-10) cc_final: 0.8356 (m-80) REVERT: A 1123 MET cc_start: 0.8423 (ttm) cc_final: 0.8005 (ttm) REVERT: B 201 PHE cc_start: 0.8890 (m-80) cc_final: 0.8600 (t80) REVERT: B 218 PHE cc_start: 0.7853 (p90) cc_final: 0.7409 (p90) REVERT: B 272 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8544 (tp30) REVERT: B 291 PHE cc_start: 0.7549 (m-80) cc_final: 0.7199 (m-80) REVERT: B 346 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7763 (ttp-170) REVERT: B 361 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8474 (mttt) REVERT: B 375 HIS cc_start: 0.8782 (m90) cc_final: 0.8272 (m90) REVERT: B 382 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6448 (t80) REVERT: B 391 MET cc_start: 0.8935 (tpp) cc_final: 0.8422 (tpp) REVERT: B 426 MET cc_start: 0.9153 (mmm) cc_final: 0.8821 (mmm) REVERT: B 552 MET cc_start: 0.7874 (tpp) cc_final: 0.7374 (tpp) REVERT: B 561 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5790 (t80) REVERT: B 595 MET cc_start: 0.8110 (mmp) cc_final: 0.7339 (mmp) REVERT: B 765 ASP cc_start: 0.8578 (m-30) cc_final: 0.8180 (t70) REVERT: B 781 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 832 MET cc_start: 0.8363 (mmm) cc_final: 0.8090 (tpt) REVERT: B 893 GLU cc_start: 0.8637 (pp20) cc_final: 0.7544 (tp30) REVERT: B 894 LEU cc_start: 0.9625 (mt) cc_final: 0.9135 (mm) REVERT: B 900 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9049 (mmm) REVERT: B 953 TYR cc_start: 0.9055 (m-10) cc_final: 0.8350 (m-80) REVERT: B 1123 MET cc_start: 0.8425 (ttm) cc_final: 0.8001 (ttm) REVERT: C 201 PHE cc_start: 0.8877 (m-80) cc_final: 0.8604 (t80) REVERT: C 218 PHE cc_start: 0.7849 (p90) cc_final: 0.7404 (p90) REVERT: C 272 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8543 (tp30) REVERT: C 291 PHE cc_start: 0.7675 (m-80) cc_final: 0.7337 (m-80) REVERT: C 346 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7763 (ttp-170) REVERT: C 361 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8478 (mttt) REVERT: C 375 HIS cc_start: 0.8770 (m90) cc_final: 0.8262 (m90) REVERT: C 382 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6454 (t80) REVERT: C 391 MET cc_start: 0.8934 (tpp) cc_final: 0.8421 (tpp) REVERT: C 426 MET cc_start: 0.9151 (mmm) cc_final: 0.8820 (mmm) REVERT: C 552 MET cc_start: 0.7888 (tpp) cc_final: 0.7391 (tpp) REVERT: C 561 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.5792 (t80) REVERT: C 595 MET cc_start: 0.8102 (mmp) cc_final: 0.7334 (mmp) REVERT: C 765 ASP cc_start: 0.8575 (m-30) cc_final: 0.8176 (t70) REVERT: C 781 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: C 832 MET cc_start: 0.8363 (mmm) cc_final: 0.8089 (tpt) REVERT: C 893 GLU cc_start: 0.8640 (pp20) cc_final: 0.7554 (tp30) REVERT: C 894 LEU cc_start: 0.9628 (mt) cc_final: 0.9142 (mm) REVERT: C 900 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: C 953 TYR cc_start: 0.9056 (m-10) cc_final: 0.8353 (m-80) REVERT: C 1123 MET cc_start: 0.8423 (ttm) cc_final: 0.8001 (ttm) REVERT: D 201 PHE cc_start: 0.8891 (m-80) cc_final: 0.8598 (t80) REVERT: D 218 PHE cc_start: 0.7867 (p90) cc_final: 0.7419 (p90) REVERT: D 272 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8521 (tp30) REVERT: D 291 PHE cc_start: 0.7623 (m-80) cc_final: 0.7307 (m-80) REVERT: D 303 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 346 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7761 (ttp-170) REVERT: D 355 LEU cc_start: 0.9361 (tp) cc_final: 0.9062 (mp) REVERT: D 361 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8468 (mttt) REVERT: D 375 HIS cc_start: 0.8757 (m90) cc_final: 0.8250 (m90) REVERT: D 382 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6414 (t80) REVERT: D 426 MET cc_start: 0.9150 (mmm) cc_final: 0.8818 (mmm) REVERT: D 471 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7903 (mm) REVERT: D 552 MET cc_start: 0.7885 (tpp) cc_final: 0.7387 (tpp) REVERT: D 561 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5788 (t80) REVERT: D 595 MET cc_start: 0.8112 (mmp) cc_final: 0.7335 (mmp) REVERT: D 765 ASP cc_start: 0.8576 (m-30) cc_final: 0.8175 (t70) REVERT: D 781 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: D 832 MET cc_start: 0.8364 (mmm) cc_final: 0.8091 (tpt) REVERT: D 893 GLU cc_start: 0.8632 (pp20) cc_final: 0.7537 (tp30) REVERT: D 894 LEU cc_start: 0.9626 (mt) cc_final: 0.9138 (mm) REVERT: D 900 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9011 (mmm) REVERT: D 953 TYR cc_start: 0.9051 (m-10) cc_final: 0.8469 (m-80) REVERT: D 1123 MET cc_start: 0.8422 (ttm) cc_final: 0.8001 (ttm) outliers start: 101 outliers final: 61 residues processed: 588 average time/residue: 0.1564 time to fit residues: 155.8489 Evaluate side-chains 574 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 494 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 382 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 382 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 26 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 341 optimal weight: 0.0970 chunk 155 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 328 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 789 ASN A1137 ASN B 475 ASN B 789 ASN B1137 ASN C 475 ASN C1137 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN D1137 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.085275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068042 restraints weight = 102564.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070592 restraints weight = 51199.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072311 restraints weight = 31298.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073445 restraints weight = 21882.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074368 restraints weight = 16755.165| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29024 Z= 0.123 Angle : 0.799 14.211 39320 Z= 0.358 Chirality : 0.046 0.334 4444 Planarity : 0.004 0.045 4924 Dihedral : 4.455 17.401 3836 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.36 % Allowed : 21.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3456 helix: 0.15 (0.13), residues: 1608 sheet: -0.73 (0.29), residues: 316 loop : -0.94 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 966 TYR 0.038 0.001 TYR A 285 PHE 0.042 0.002 PHE A 291 TRP 0.010 0.001 TRP C 304 HIS 0.004 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00289 (29024) covalent geometry : angle 0.79887 (39320) hydrogen bonds : bond 0.03639 ( 1128) hydrogen bonds : angle 4.66300 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 525 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.8618 (mttt) cc_final: 0.8174 (tmtt) REVERT: A 201 PHE cc_start: 0.8836 (m-80) cc_final: 0.8617 (t80) REVERT: A 218 PHE cc_start: 0.7735 (p90) cc_final: 0.7137 (p90) REVERT: A 272 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8545 (tp30) REVERT: A 291 PHE cc_start: 0.7561 (m-80) cc_final: 0.7241 (m-80) REVERT: A 346 ARG cc_start: 0.8321 (ttm170) cc_final: 0.7825 (ttp-170) REVERT: A 361 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8446 (mttt) REVERT: A 375 HIS cc_start: 0.8732 (m90) cc_final: 0.8229 (m90) REVERT: A 382 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6315 (t80) REVERT: A 391 MET cc_start: 0.8849 (tpp) cc_final: 0.8086 (tpp) REVERT: A 426 MET cc_start: 0.9135 (mmm) cc_final: 0.8829 (mmm) REVERT: A 552 MET cc_start: 0.7752 (tpp) cc_final: 0.7216 (tpp) REVERT: A 561 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5809 (t80) REVERT: A 595 MET cc_start: 0.7586 (mmp) cc_final: 0.7232 (mmp) REVERT: A 765 ASP cc_start: 0.8585 (m-30) cc_final: 0.8266 (t70) REVERT: A 781 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 832 MET cc_start: 0.8381 (mmm) cc_final: 0.8080 (tpt) REVERT: A 851 ASP cc_start: 0.8518 (m-30) cc_final: 0.8069 (t0) REVERT: A 893 GLU cc_start: 0.8626 (pp20) cc_final: 0.7547 (tp30) REVERT: A 894 LEU cc_start: 0.9618 (mt) cc_final: 0.9145 (mm) REVERT: A 900 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9007 (mmm) REVERT: A 953 TYR cc_start: 0.8978 (m-10) cc_final: 0.8393 (m-80) REVERT: A 1123 MET cc_start: 0.8415 (ttm) cc_final: 0.7961 (ttm) REVERT: A 1137 ASN cc_start: 0.7541 (m-40) cc_final: 0.7225 (m-40) REVERT: B 179 LYS cc_start: 0.8623 (mttt) cc_final: 0.8179 (tmtt) REVERT: B 201 PHE cc_start: 0.8803 (m-80) cc_final: 0.8519 (t80) REVERT: B 218 PHE cc_start: 0.7748 (p90) cc_final: 0.7138 (p90) REVERT: B 272 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8578 (tp30) REVERT: B 291 PHE cc_start: 0.7505 (m-80) cc_final: 0.7281 (m-80) REVERT: B 346 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7823 (ttp-170) REVERT: B 361 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8444 (mttt) REVERT: B 375 HIS cc_start: 0.8733 (m90) cc_final: 0.8226 (m90) REVERT: B 382 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6303 (t80) REVERT: B 391 MET cc_start: 0.8941 (tpp) cc_final: 0.8403 (tpp) REVERT: B 426 MET cc_start: 0.9145 (mmm) cc_final: 0.8841 (mmm) REVERT: B 552 MET cc_start: 0.7738 (tpp) cc_final: 0.7199 (tpp) REVERT: B 561 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.5814 (t80) REVERT: B 595 MET cc_start: 0.7566 (mmp) cc_final: 0.7230 (mmp) REVERT: B 765 ASP cc_start: 0.8588 (m-30) cc_final: 0.8269 (t70) REVERT: B 781 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 832 MET cc_start: 0.8385 (mmm) cc_final: 0.8083 (tpt) REVERT: B 851 ASP cc_start: 0.8517 (m-30) cc_final: 0.8064 (t0) REVERT: B 893 GLU cc_start: 0.8633 (pp20) cc_final: 0.7555 (tp30) REVERT: B 894 LEU cc_start: 0.9620 (mt) cc_final: 0.9150 (mm) REVERT: B 900 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9006 (mmm) REVERT: B 953 TYR cc_start: 0.8984 (m-10) cc_final: 0.8387 (m-80) REVERT: B 1123 MET cc_start: 0.8405 (ttm) cc_final: 0.7956 (ttm) REVERT: B 1137 ASN cc_start: 0.7582 (m-40) cc_final: 0.7257 (m-40) REVERT: C 179 LYS cc_start: 0.8620 (mttt) cc_final: 0.8176 (tmtt) REVERT: C 201 PHE cc_start: 0.8842 (m-80) cc_final: 0.8621 (t80) REVERT: C 218 PHE cc_start: 0.7737 (p90) cc_final: 0.7125 (p90) REVERT: C 272 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8575 (tp30) REVERT: C 291 PHE cc_start: 0.7440 (m-80) cc_final: 0.7220 (m-80) REVERT: C 346 ARG cc_start: 0.8320 (ttm170) cc_final: 0.7825 (ttp-170) REVERT: C 361 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8450 (mttt) REVERT: C 375 HIS cc_start: 0.8720 (m90) cc_final: 0.8218 (m90) REVERT: C 382 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6311 (t80) REVERT: C 391 MET cc_start: 0.8946 (tpp) cc_final: 0.8401 (tpp) REVERT: C 426 MET cc_start: 0.9138 (mmm) cc_final: 0.8838 (mmm) REVERT: C 552 MET cc_start: 0.7748 (tpp) cc_final: 0.7207 (tpp) REVERT: C 561 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.5810 (t80) REVERT: C 595 MET cc_start: 0.7581 (mmp) cc_final: 0.7237 (mmp) REVERT: C 765 ASP cc_start: 0.8587 (m-30) cc_final: 0.8266 (t70) REVERT: C 781 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: C 832 MET cc_start: 0.8376 (mmm) cc_final: 0.8074 (tpt) REVERT: C 851 ASP cc_start: 0.8523 (m-30) cc_final: 0.8067 (t0) REVERT: C 893 GLU cc_start: 0.8632 (pp20) cc_final: 0.7555 (tp30) REVERT: C 894 LEU cc_start: 0.9621 (mt) cc_final: 0.9153 (mm) REVERT: C 900 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8991 (mmm) REVERT: C 953 TYR cc_start: 0.8982 (m-10) cc_final: 0.8387 (m-80) REVERT: C 1123 MET cc_start: 0.8408 (ttm) cc_final: 0.7960 (ttm) REVERT: C 1137 ASN cc_start: 0.7577 (m-40) cc_final: 0.7253 (m-40) REVERT: D 179 LYS cc_start: 0.8621 (mttt) cc_final: 0.8177 (tmtt) REVERT: D 201 PHE cc_start: 0.8808 (m-80) cc_final: 0.8523 (t80) REVERT: D 218 PHE cc_start: 0.7746 (p90) cc_final: 0.7126 (p90) REVERT: D 272 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8550 (tp30) REVERT: D 291 PHE cc_start: 0.7605 (m-80) cc_final: 0.7391 (m-80) REVERT: D 303 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8496 (mt) REVERT: D 346 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7822 (ttp-170) REVERT: D 355 LEU cc_start: 0.9324 (tp) cc_final: 0.9069 (mp) REVERT: D 361 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8440 (mttt) REVERT: D 375 HIS cc_start: 0.8822 (m90) cc_final: 0.8273 (m90) REVERT: D 382 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6214 (t80) REVERT: D 426 MET cc_start: 0.9134 (mmm) cc_final: 0.8828 (mmm) REVERT: D 561 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5809 (t80) REVERT: D 595 MET cc_start: 0.7573 (mmp) cc_final: 0.7228 (mmp) REVERT: D 765 ASP cc_start: 0.8587 (m-30) cc_final: 0.8261 (t70) REVERT: D 781 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: D 832 MET cc_start: 0.8448 (mmm) cc_final: 0.8099 (tpt) REVERT: D 893 GLU cc_start: 0.8627 (pp20) cc_final: 0.7408 (tp30) REVERT: D 894 LEU cc_start: 0.9614 (mt) cc_final: 0.9211 (mm) REVERT: D 900 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8981 (mmm) REVERT: D 953 TYR cc_start: 0.9019 (m-10) cc_final: 0.8430 (m-80) REVERT: D 1123 MET cc_start: 0.8411 (ttm) cc_final: 0.7966 (ttm) REVERT: D 1137 ASN cc_start: 0.7526 (m-40) cc_final: 0.7216 (m-40) outliers start: 74 outliers final: 51 residues processed: 581 average time/residue: 0.1548 time to fit residues: 152.4639 Evaluate side-chains 558 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 490 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 382 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 382 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 139 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 19 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 789 ASN C 789 ASN ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.085145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067935 restraints weight = 103256.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070433 restraints weight = 52637.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072121 restraints weight = 32641.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.073200 restraints weight = 22937.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074151 restraints weight = 17789.827| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29024 Z= 0.128 Angle : 0.818 15.174 39320 Z= 0.371 Chirality : 0.046 0.373 4444 Planarity : 0.004 0.045 4924 Dihedral : 4.435 16.991 3836 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.75 % Allowed : 22.13 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3456 helix: 0.29 (0.13), residues: 1572 sheet: -0.51 (0.29), residues: 340 loop : -0.93 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 966 TYR 0.019 0.001 TYR B 285 PHE 0.037 0.002 PHE A 291 TRP 0.018 0.001 TRP D 332 HIS 0.004 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00302 (29024) covalent geometry : angle 0.81777 (39320) hydrogen bonds : bond 0.03684 ( 1128) hydrogen bonds : angle 4.77480 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5041.23 seconds wall clock time: 88 minutes 8.81 seconds (5288.81 seconds total)