Starting phenix.real_space_refine on Sun Oct 12 02:58:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.map" model { file = "/net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ez8_3984/10_2025/6ez8_3984.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 129 5.16 5 C 13129 2.51 5 N 3524 2.21 5 O 3709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20491 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2353, 18458 Classifications: {'peptide': 2353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 106, 'TRANS': 2246} Chain breaks: 19 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2033 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.15, per 1000 atoms: 0.25 Number of scatterers: 20491 At special positions: 0 Unit cell: (140.4, 108, 147.15, 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 129 16.00 O 3709 8.00 N 3524 7.00 C 13129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 768 " - pdb=" SG CYS A 803 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5014 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 0 sheets defined 57.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.946A pdb=" N ASN A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 107 " --> pdb=" O CYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.962A pdb=" N LEU A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 121 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 124' Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.959A pdb=" N LEU A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.875A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 153' Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.716A pdb=" N LEU A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.929A pdb=" N ALA A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 182' Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.969A pdb=" N ALA A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 188 " --> pdb=" O TRP A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 188' Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.503A pdb=" N LEU A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 193' Processing helix chain 'A' and resid 197 through 204 removed outlier: 3.727A pdb=" N TYR A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.918A pdb=" N CYS A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 212 " --> pdb=" O CYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.996A pdb=" N THR A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.977A pdb=" N SER A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 removed outlier: 3.815A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 253' Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.959A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.910A pdb=" N ALA A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 274' Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.877A pdb=" N LEU A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 292' Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.878A pdb=" N VAL A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 311' Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.945A pdb=" N VAL A 353 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 359' Processing helix chain 'A' and resid 384 through 393 removed outlier: 3.957A pdb=" N GLN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.938A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 687 removed outlier: 3.872A pdb=" N VAL A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 683 " --> pdb=" O HIS A 679 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 684 " --> pdb=" O CYS A 680 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 720 removed outlier: 3.865A pdb=" N VAL A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 718 " --> pdb=" O CYS A 714 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 711 through 720' Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 768 through 777 removed outlier: 3.803A pdb=" N ILE A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 774 " --> pdb=" O THR A 770 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 792 removed outlier: 3.906A pdb=" N MET A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 788 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 790 " --> pdb=" O TRP A 786 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 791 " --> pdb=" O MET A 787 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.841A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.802A pdb=" N LEU A 833 " --> pdb=" O CYS A 829 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 834' Processing helix chain 'A' and resid 840 through 850 removed outlier: 4.003A pdb=" N GLN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 4.325A pdb=" N ASN A 854 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 855 " --> pdb=" O LEU A 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 855' Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.981A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 882 " --> pdb=" O PHE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 893 removed outlier: 4.138A pdb=" N HIS A 892 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 893 " --> pdb=" O ALA A 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 893' Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.667A pdb=" N ARG A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.762A pdb=" N ASP A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.945A pdb=" N HIS A 921 " --> pdb=" O PRO A 917 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 922 " --> pdb=" O ARG A 918 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 Processing helix chain 'A' and resid 931 through 934 removed outlier: 4.130A pdb=" N LEU A 934 " --> pdb=" O VAL A 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 931 through 934' Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.920A pdb=" N VAL A 949 " --> pdb=" O PRO A 945 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 945 through 950' Processing helix chain 'A' and resid 993 through 998 removed outlier: 3.894A pdb=" N ASN A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 993 through 998' Processing helix chain 'A' and resid 1014 through 1020 removed outlier: 3.861A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1014 through 1020' Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.284A pdb=" N ILE A1066 " --> pdb=" O MET A1062 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A1068 " --> pdb=" O THR A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1077 removed outlier: 3.576A pdb=" N LEU A1077 " --> pdb=" O TRP A1074 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1074 through 1077' Processing helix chain 'A' and resid 1078 through 1083 removed outlier: 3.924A pdb=" N GLN A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 4.568A pdb=" N LEU A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1141 removed outlier: 3.509A pdb=" N VAL A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 3.637A pdb=" N LEU A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1237 removed outlier: 3.531A pdb=" N ASP A1237 " --> pdb=" O ARG A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1275 removed outlier: 3.816A pdb=" N GLN A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A1273 " --> pdb=" O VAL A1269 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A1274 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A1275 " --> pdb=" O SER A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1268 through 1275' Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1285 through 1296 removed outlier: 3.924A pdb=" N LEU A1290 " --> pdb=" O VAL A1286 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A1291 " --> pdb=" O GLU A1287 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A1292 " --> pdb=" O GLU A1288 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A1294 " --> pdb=" O LEU A1290 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A1295 " --> pdb=" O GLY A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 3.925A pdb=" N GLN A1310 " --> pdb=" O VAL A1306 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A1311 " --> pdb=" O CYS A1307 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1312 " --> pdb=" O VAL A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.903A pdb=" N THR A1360 " --> pdb=" O MET A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1368 removed outlier: 3.923A pdb=" N ALA A1367 " --> pdb=" O THR A1363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1363 through 1368' Processing helix chain 'A' and resid 1421 through 1433 removed outlier: 3.727A pdb=" N ILE A1426 " --> pdb=" O GLU A1422 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A1427 " --> pdb=" O PRO A1423 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1428 " --> pdb=" O LEU A1424 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A1429 " --> pdb=" O VAL A1425 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A1430 " --> pdb=" O ILE A1426 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1431 " --> pdb=" O LYS A1427 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1433 " --> pdb=" O LEU A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1474 removed outlier: 3.866A pdb=" N VAL A1471 " --> pdb=" O PHE A1467 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1472 " --> pdb=" O ILE A1468 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A1473 " --> pdb=" O GLY A1469 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN A1474 " --> pdb=" O PHE A1470 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1467 through 1474' Processing helix chain 'A' and resid 1475 through 1480 removed outlier: 3.901A pdb=" N GLU A1479 " --> pdb=" O PHE A1475 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1475 through 1480' Processing helix chain 'A' and resid 1485 through 1488 removed outlier: 3.580A pdb=" N ALA A1488 " --> pdb=" O GLU A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1485 through 1488' Processing helix chain 'A' and resid 1489 through 1499 removed outlier: 3.950A pdb=" N PHE A1494 " --> pdb=" O ILE A1490 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A1495 " --> pdb=" O PRO A1491 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A1496 " --> pdb=" O ASN A1492 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1497 " --> pdb=" O ILE A1493 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A1498 " --> pdb=" O PHE A1494 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A1499 " --> pdb=" O PHE A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1526 removed outlier: 3.883A pdb=" N ILE A1517 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A1518 " --> pdb=" O PRO A1514 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A1519 " --> pdb=" O LYS A1515 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A1521 " --> pdb=" O ILE A1517 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A1522 " --> pdb=" O GLN A1518 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A1523 " --> pdb=" O LEU A1519 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A1524 " --> pdb=" O CYS A1520 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A1525 " --> pdb=" O ASP A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1544 removed outlier: 3.970A pdb=" N HIS A1543 " --> pdb=" O GLN A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1573 removed outlier: 3.972A pdb=" N THR A1562 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A1563 " --> pdb=" O GLU A1559 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A1564 " --> pdb=" O LEU A1560 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A1565 " --> pdb=" O GLU A1561 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A1566 " --> pdb=" O THR A1562 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1567 " --> pdb=" O GLN A1563 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A1568 " --> pdb=" O LYS A1564 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET A1570 " --> pdb=" O VAL A1566 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A1571 " --> pdb=" O VAL A1567 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A1572 " --> pdb=" O VAL A1568 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1558 through 1573' Processing helix chain 'A' and resid 1579 through 1584 removed outlier: 3.951A pdb=" N MET A1583 " --> pdb=" O GLN A1579 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A1584 " --> pdb=" O VAL A1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1579 through 1584' Processing helix chain 'A' and resid 1584 through 1595 removed outlier: 3.789A pdb=" N LEU A1588 " --> pdb=" O PHE A1584 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A1589 " --> pdb=" O ILE A1585 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A1590 " --> pdb=" O LEU A1586 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A1591 " --> pdb=" O VAL A1587 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A1592 " --> pdb=" O LEU A1588 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A1593 " --> pdb=" O GLN A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1606 removed outlier: 3.928A pdb=" N LYS A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A1601 " --> pdb=" O ASP A1597 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1602 " --> pdb=" O LYS A1598 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A1603 " --> pdb=" O TRP A1599 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A1604 " --> pdb=" O LYS A1600 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A1605 " --> pdb=" O ARG A1601 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A1606 " --> pdb=" O LEU A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1606 through 1614 removed outlier: 3.848A pdb=" N ILE A1610 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1611 " --> pdb=" O ALA A1607 " (cutoff:3.500A) Proline residue: A1612 - end of helix No H-bonds generated for 'chain 'A' and resid 1606 through 1614' Processing helix chain 'A' and resid 1625 through 1632 removed outlier: 3.933A pdb=" N VAL A1629 " --> pdb=" O GLU A1625 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A1630 " --> pdb=" O ALA A1626 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A1631 " --> pdb=" O LEU A1627 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A1632 " --> pdb=" O GLY A1628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1625 through 1632' Processing helix chain 'A' and resid 1632 through 1637 removed outlier: 3.927A pdb=" N ILE A1636 " --> pdb=" O THR A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1651 removed outlier: 3.826A pdb=" N LEU A1649 " --> pdb=" O VAL A1645 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A1650 " --> pdb=" O ASP A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1675 removed outlier: 3.842A pdb=" N ALA A1674 " --> pdb=" O SER A1670 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A1675 " --> pdb=" O GLY A1671 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1670 through 1675' Processing helix chain 'A' and resid 1677 through 1682 removed outlier: 3.958A pdb=" N SER A1681 " --> pdb=" O ARG A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1693 removed outlier: 3.940A pdb=" N VAL A1688 " --> pdb=" O THR A1684 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A1689 " --> pdb=" O GLU A1685 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A1690 " --> pdb=" O ASP A1686 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A1691 " --> pdb=" O ILE A1687 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A1692 " --> pdb=" O VAL A1688 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A1693 " --> pdb=" O LEU A1689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1684 through 1693' Processing helix chain 'A' and resid 1707 through 1713 removed outlier: 3.871A pdb=" N ARG A1711 " --> pdb=" O ILE A1707 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP A1712 " --> pdb=" O ASN A1708 " (cutoff:3.500A) Processing helix chain 'A' and resid 1731 through 1741 removed outlier: 3.937A pdb=" N PHE A1736 " --> pdb=" O PRO A1732 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A1737 " --> pdb=" O GLU A1733 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A1738 " --> pdb=" O GLU A1734 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A1739 " --> pdb=" O THR A1735 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A1740 " --> pdb=" O PHE A1736 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A1741 " --> pdb=" O SER A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1752 removed outlier: 3.875A pdb=" N ILE A1751 " --> pdb=" O LEU A1747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1747 through 1752' Processing helix chain 'A' and resid 1762 through 1767 removed outlier: 3.945A pdb=" N PHE A1767 " --> pdb=" O GLN A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1783 removed outlier: 3.855A pdb=" N ILE A1782 " --> pdb=" O CYS A1778 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A1783 " --> pdb=" O LEU A1779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1778 through 1783' Processing helix chain 'A' and resid 1788 through 1800 removed outlier: 4.016A pdb=" N THR A1792 " --> pdb=" O PHE A1788 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1793 " --> pdb=" O ARG A1789 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1794 " --> pdb=" O ARG A1790 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A1796 " --> pdb=" O THR A1792 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1819 removed outlier: 4.042A pdb=" N ARG A1817 " --> pdb=" O SER A1813 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A1818 " --> pdb=" O LEU A1814 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A1819 " --> pdb=" O ASN A1815 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1813 through 1819' Processing helix chain 'A' and resid 1832 through 1837 removed outlier: 3.865A pdb=" N LEU A1836 " --> pdb=" O TRP A1832 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A1837 " --> pdb=" O CYS A1833 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1832 through 1837' Processing helix chain 'A' and resid 1845 through 1850 removed outlier: 4.023A pdb=" N GLU A1849 " --> pdb=" O ARG A1845 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A1850 " --> pdb=" O TRP A1846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1845 through 1850' Processing helix chain 'A' and resid 1887 through 1892 Processing helix chain 'A' and resid 1899 through 1905 removed outlier: 3.727A pdb=" N GLN A1904 " --> pdb=" O ASP A1900 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A1905 " --> pdb=" O TYR A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1918 removed outlier: 3.894A pdb=" N LEU A1915 " --> pdb=" O HIS A1911 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A1916 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A1917 " --> pdb=" O THR A1913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1925 removed outlier: 3.939A pdb=" N SER A1925 " --> pdb=" O GLN A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1942 removed outlier: 3.900A pdb=" N ILE A1936 " --> pdb=" O VAL A1932 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A1937 " --> pdb=" O GLN A1933 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1938 " --> pdb=" O ASP A1934 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A1939 " --> pdb=" O PHE A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1954 removed outlier: 3.969A pdb=" N GLY A1947 " --> pdb=" O SER A1943 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A1948 " --> pdb=" O ALA A1944 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A1949 " --> pdb=" O ALA A1945 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A1950 " --> pdb=" O SER A1946 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A1951 " --> pdb=" O GLY A1947 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A1952 " --> pdb=" O LEU A1948 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A1953 " --> pdb=" O PHE A1949 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN A1954 " --> pdb=" O ILE A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1971 removed outlier: 3.930A pdb=" N LEU A1970 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A1971 " --> pdb=" O LYS A1967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1966 through 1971' Processing helix chain 'A' and resid 1977 through 1981 removed outlier: 3.697A pdb=" N SER A1981 " --> pdb=" O LEU A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1991 removed outlier: 3.587A pdb=" N ARG A1991 " --> pdb=" O LEU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1995 removed outlier: 3.852A pdb=" N THR A1995 " --> pdb=" O LEU A1992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1992 through 1995' Processing helix chain 'A' and resid 2008 through 2017 removed outlier: 3.921A pdb=" N VAL A2012 " --> pdb=" O ALA A2008 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A2013 " --> pdb=" O CYS A2009 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A2014 " --> pdb=" O ARG A2010 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A2015 " --> pdb=" O ARG A2011 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A2016 " --> pdb=" O VAL A2012 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A2017 " --> pdb=" O GLU A2013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2008 through 2017' Processing helix chain 'A' and resid 2019 through 2025 removed outlier: 3.666A pdb=" N SER A2023 " --> pdb=" O ASN A2019 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET A2024 " --> pdb=" O LEU A2020 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A2025 " --> pdb=" O GLN A2021 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2019 through 2025' Processing helix chain 'A' and resid 2028 through 2037 removed outlier: 3.942A pdb=" N ASN A2033 " --> pdb=" O MET A2029 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A2034 " --> pdb=" O GLU A2030 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A2035 " --> pdb=" O GLU A2031 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A2036 " --> pdb=" O LEU A2032 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A2037 " --> pdb=" O ASN A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2037 through 2042 removed outlier: 3.943A pdb=" N SER A2041 " --> pdb=" O GLU A2037 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A2042 " --> pdb=" O TYR A2038 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2037 through 2042' Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2062 removed outlier: 3.724A pdb=" N TYR A2052 " --> pdb=" O HIS A2048 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A2054 " --> pdb=" O ARG A2050 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A2055 " --> pdb=" O LEU A2051 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A2056 " --> pdb=" O TYR A2052 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A2057 " --> pdb=" O SER A2053 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A2059 " --> pdb=" O LEU A2055 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A2060 " --> pdb=" O ASP A2056 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A2061 " --> pdb=" O ARG A2057 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A2062 " --> pdb=" O PHE A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2100 removed outlier: 3.949A pdb=" N HIS A2098 " --> pdb=" O ASP A2094 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A2099 " --> pdb=" O TRP A2095 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A2100 " --> pdb=" O TYR A2096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2094 through 2100' Processing helix chain 'A' and resid 2101 through 2104 Processing helix chain 'A' and resid 2112 through 2119 removed outlier: 3.978A pdb=" N GLU A2117 " --> pdb=" O LEU A2113 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A2118 " --> pdb=" O GLU A2114 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A2119 " --> pdb=" O GLY A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2132 Processing helix chain 'A' and resid 2142 through 2155 removed outlier: 3.964A pdb=" N SER A2146 " --> pdb=" O ALA A2142 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A2147 " --> pdb=" O PRO A2143 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A2148 " --> pdb=" O CYS A2144 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A2149 " --> pdb=" O LEU A2145 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A2150 " --> pdb=" O SER A2146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A2151 " --> pdb=" O LEU A2147 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A2152 " --> pdb=" O GLY A2148 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A2154 " --> pdb=" O SER A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2178 removed outlier: 3.955A pdb=" N ALA A2163 " --> pdb=" O ALA A2159 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A2164 " --> pdb=" O LEU A2160 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A2165 " --> pdb=" O PHE A2161 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A2166 " --> pdb=" O GLU A2162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A2167 " --> pdb=" O ALA A2163 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A2168 " --> pdb=" O ALA A2164 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A2169 " --> pdb=" O ARG A2165 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A2170 " --> pdb=" O GLU A2166 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A2171 " --> pdb=" O VAL A2167 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A2172 " --> pdb=" O THR A2168 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A2173 " --> pdb=" O LEU A2169 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A2174 " --> pdb=" O ALA A2170 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A2175 " --> pdb=" O ARG A2171 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A2176 " --> pdb=" O VAL A2172 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2203 removed outlier: 4.225A pdb=" N TRP A2198 " --> pdb=" O ALA A2195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A2201 " --> pdb=" O TRP A2198 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A2202 " --> pdb=" O SER A2199 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2217 removed outlier: 3.989A pdb=" N SER A2213 " --> pdb=" O ALA A2209 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A2214 " --> pdb=" O LEU A2210 " (cutoff:3.500A) Proline residue: A2215 - end of helix No H-bonds generated for 'chain 'A' and resid 2209 through 2217' Processing helix chain 'A' and resid 2219 through 2227 removed outlier: 3.890A pdb=" N GLN A2223 " --> pdb=" O ARG A2219 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A2224 " --> pdb=" O ALA A2220 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A2225 " --> pdb=" O LEU A2221 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A2226 " --> pdb=" O ALA A2222 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A2227 " --> pdb=" O GLN A2223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2219 through 2227' Processing helix chain 'A' and resid 2228 through 2231 removed outlier: 3.683A pdb=" N LEU A2231 " --> pdb=" O VAL A2228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2228 through 2231' Processing helix chain 'A' and resid 2239 through 2241 No H-bonds generated for 'chain 'A' and resid 2239 through 2241' Processing helix chain 'A' and resid 2242 through 2247 Processing helix chain 'A' and resid 2248 through 2253 removed outlier: 3.767A pdb=" N THR A2252 " --> pdb=" O PHE A2248 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A2253 " --> pdb=" O VAL A2249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2248 through 2253' Processing helix chain 'A' and resid 2256 through 2263 removed outlier: 3.948A pdb=" N LEU A2260 " --> pdb=" O LEU A2256 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A2261 " --> pdb=" O SER A2257 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A2262 " --> pdb=" O TRP A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2273 through 2282 removed outlier: 3.950A pdb=" N CYS A2277 " --> pdb=" O ALA A2273 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A2278 " --> pdb=" O GLY A2274 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS A2279 " --> pdb=" O LEU A2275 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A2280 " --> pdb=" O ASP A2276 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A2281 " --> pdb=" O CYS A2277 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A2282 " --> pdb=" O CYS A2278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2273 through 2282' Processing helix chain 'A' and resid 2284 through 2291 removed outlier: 3.963A pdb=" N SER A2289 " --> pdb=" O PRO A2285 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A2290 " --> pdb=" O GLY A2286 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A2291 " --> pdb=" O LEU A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2292 through 2295 removed outlier: 6.219A pdb=" N GLU A2295 " --> pdb=" O SER A2292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2292 through 2295' Processing helix chain 'A' and resid 2296 through 2301 removed outlier: 3.523A pdb=" N ALA A2300 " --> pdb=" O PHE A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2316 removed outlier: 3.710A pdb=" N VAL A2314 " --> pdb=" O ILE A2310 " (cutoff:3.500A) Processing helix chain 'A' and resid 2349 through 2364 removed outlier: 4.047A pdb=" N THR A2353 " --> pdb=" O PRO A2349 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A2359 " --> pdb=" O ALA A2355 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A2360 " --> pdb=" O CYS A2356 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A2361 " --> pdb=" O GLU A2357 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET A2362 " --> pdb=" O MET A2358 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A2363 " --> pdb=" O VAL A2359 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A2364 " --> pdb=" O ALA A2360 " (cutoff:3.500A) Processing helix chain 'A' and resid 2364 through 2369 removed outlier: 3.986A pdb=" N SER A2368 " --> pdb=" O GLU A2364 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2379 removed outlier: 3.953A pdb=" N SER A2378 " --> pdb=" O LYS A2375 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY A2379 " --> pdb=" O ARG A2376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2375 through 2379' Processing helix chain 'A' and resid 2388 through 2394 removed outlier: 3.886A pdb=" N ILE A2392 " --> pdb=" O LEU A2388 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A2393 " --> pdb=" O ARG A2389 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A2394 " --> pdb=" O ASN A2390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2388 through 2394' Processing helix chain 'A' and resid 2401 through 2406 removed outlier: 3.854A pdb=" N THR A2405 " --> pdb=" O VAL A2401 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A2406 " --> pdb=" O ASN A2402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2401 through 2406' Processing helix chain 'A' and resid 2408 through 2414 removed outlier: 4.181A pdb=" N TRP A2412 " --> pdb=" O PRO A2408 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A2413 " --> pdb=" O PRO A2409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A2414 " --> pdb=" O LEU A2410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2408 through 2414' Processing helix chain 'A' and resid 2432 through 2436 removed outlier: 3.598A pdb=" N PHE A2435 " --> pdb=" O PRO A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2446 removed outlier: 3.970A pdb=" N GLU A2444 " --> pdb=" O GLU A2440 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A2445 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A2446 " --> pdb=" O PHE A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2446 through 2451 removed outlier: 3.878A pdb=" N ASN A2450 " --> pdb=" O ILE A2446 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A2451 " --> pdb=" O TYR A2447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2446 through 2451' Processing helix chain 'A' and resid 2456 through 2458 No H-bonds generated for 'chain 'A' and resid 2456 through 2458' Processing helix chain 'A' and resid 2459 through 2469 removed outlier: 3.970A pdb=" N THR A2463 " --> pdb=" O GLN A2459 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP A2464 " --> pdb=" O PHE A2460 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A2465 " --> pdb=" O GLU A2461 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A2466 " --> pdb=" O GLU A2462 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A2467 " --> pdb=" O THR A2463 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A2468 " --> pdb=" O TRP A2464 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A2469 " --> pdb=" O ALA A2465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2459 through 2469' Processing helix chain 'A' and resid 2492 through 2497 removed outlier: 3.942A pdb=" N LEU A2497 " --> pdb=" O GLN A2493 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2508 removed outlier: 3.860A pdb=" N THR A2503 " --> pdb=" O VAL A2499 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A2504 " --> pdb=" O GLN A2500 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2505 " --> pdb=" O ALA A2501 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A2506 " --> pdb=" O ILE A2502 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A2507 " --> pdb=" O THR A2503 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A2508 " --> pdb=" O SER A2504 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2499 through 2508' Processing helix chain 'A' and resid 2539 through 2553 removed outlier: 3.515A pdb=" N LEU A2543 " --> pdb=" O PHE A2539 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A2544 " --> pdb=" O GLY A2540 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A2545 " --> pdb=" O ARG A2541 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A2546 " --> pdb=" O LYS A2542 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A2547 " --> pdb=" O LEU A2543 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A2548 " --> pdb=" O SER A2544 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A2549 " --> pdb=" O ILE A2545 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A2550 " --> pdb=" O ILE A2546 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A2551 " --> pdb=" O ARG A2547 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A2552 " --> pdb=" O GLY A2548 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A2553 " --> pdb=" O ILE A2549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2539 through 2553' Processing helix chain 'A' and resid 2615 through 2620 removed outlier: 3.952A pdb=" N TRP A2619 " --> pdb=" O ILE A2615 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A2620 " --> pdb=" O HIS A2616 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2615 through 2620' Processing helix chain 'A' and resid 2663 through 2678 removed outlier: 3.664A pdb=" N CYS A2667 " --> pdb=" O ASP A2663 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A2668 " --> pdb=" O ILE A2664 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A2669 " --> pdb=" O HIS A2665 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A2670 " --> pdb=" O SER A2666 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A2671 " --> pdb=" O CYS A2667 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A2672 " --> pdb=" O SER A2668 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A2673 " --> pdb=" O GLN A2669 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A2674 " --> pdb=" O PHE A2670 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A2675 " --> pdb=" O LEU A2671 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A2676 " --> pdb=" O LEU A2672 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A2677 " --> pdb=" O GLU A2673 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A2678 " --> pdb=" O LEU A2674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2663 through 2678' Processing helix chain 'A' and resid 2689 through 2703 removed outlier: 3.947A pdb=" N SER A2694 " --> pdb=" O ALA A2690 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A2695 " --> pdb=" O ILE A2691 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A2696 " --> pdb=" O LEU A2692 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A2697 " --> pdb=" O ILE A2693 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A2698 " --> pdb=" O SER A2694 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A2699 " --> pdb=" O GLU A2695 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A2700 " --> pdb=" O VAL A2696 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A2701 " --> pdb=" O VAL A2697 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A2702 " --> pdb=" O ARG A2698 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A2703 " --> pdb=" O SER A2699 " (cutoff:3.500A) Processing helix chain 'A' and resid 2704 through 2706 No H-bonds generated for 'chain 'A' and resid 2704 through 2706' Processing helix chain 'A' and resid 2709 through 2725 removed outlier: 3.878A pdb=" N GLU A2714 " --> pdb=" O ARG A2710 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A2715 " --> pdb=" O ASN A2711 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A2716 " --> pdb=" O GLN A2712 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A2717 " --> pdb=" O PHE A2713 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A2718 " --> pdb=" O GLU A2714 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A2719 " --> pdb=" O LEU A2715 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A2720 " --> pdb=" O MET A2716 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A2721 " --> pdb=" O TYR A2717 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A2722 " --> pdb=" O VAL A2718 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A2723 " --> pdb=" O THR A2719 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A2724 " --> pdb=" O LEU A2720 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A2725 " --> pdb=" O THR A2721 " (cutoff:3.500A) Processing helix chain 'A' and resid 2734 through 2749 removed outlier: 3.899A pdb=" N LEU A2738 " --> pdb=" O LEU A2734 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A2739 " --> pdb=" O ALA A2735 " (cutoff:3.500A) Proline residue: A2740 - end of helix removed outlier: 3.877A pdb=" N CYS A2743 " --> pdb=" O VAL A2739 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A2744 " --> pdb=" O PRO A2740 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A2745 " --> pdb=" O ALA A2741 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A2746 " --> pdb=" O THR A2742 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A2747 " --> pdb=" O CYS A2743 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A2748 " --> pdb=" O LYS A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2767 removed outlier: 3.969A pdb=" N GLU A2757 " --> pdb=" O LYS A2753 " (cutoff:3.500A) Proline residue: A2758 - end of helix removed outlier: 3.948A pdb=" N ARG A2761 " --> pdb=" O GLU A2757 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A2762 " --> pdb=" O PRO A2758 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A2763 " --> pdb=" O VAL A2759 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A2764 " --> pdb=" O SER A2760 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A2765 " --> pdb=" O ARG A2761 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR A2766 " --> pdb=" O LEU A2762 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A2767 " --> pdb=" O LEU A2763 " (cutoff:3.500A) Processing helix chain 'A' and resid 2773 through 2778 removed outlier: 3.890A pdb=" N GLY A2777 " --> pdb=" O PRO A2773 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A2778 " --> pdb=" O SER A2774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2773 through 2778' Processing helix chain 'A' and resid 2779 through 2788 removed outlier: 3.903A pdb=" N LEU A2783 " --> pdb=" O LEU A2779 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A2784 " --> pdb=" O HIS A2780 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A2785 " --> pdb=" O GLY A2781 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS A2788 " --> pdb=" O TYR A2784 " (cutoff:3.500A) Processing helix chain 'A' and resid 2795 through 2797 No H-bonds generated for 'chain 'A' and resid 2795 through 2797' Processing helix chain 'A' and resid 2798 through 2812 removed outlier: 3.783A pdb=" N ILE A2802 " --> pdb=" O LEU A2798 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A2804 " --> pdb=" O PRO A2800 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A2805 " --> pdb=" O VAL A2801 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A2806 " --> pdb=" O ILE A2802 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A2807 " --> pdb=" O SER A2803 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A2808 " --> pdb=" O ASP A2804 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN A2809 " --> pdb=" O TYR A2805 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A2810 " --> pdb=" O LEU A2806 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A2811 " --> pdb=" O LEU A2807 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A2812 " --> pdb=" O SER A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2824 through 2829 removed outlier: 3.842A pdb=" N MET A2828 " --> pdb=" O HIS A2824 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A2829 " --> pdb=" O VAL A2825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2824 through 2829' Processing helix chain 'A' and resid 2832 through 2839 removed outlier: 3.941A pdb=" N ILE A2836 " --> pdb=" O ALA A2832 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A2837 " --> pdb=" O PHE A2833 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A2838 " --> pdb=" O TYR A2834 " (cutoff:3.500A) Processing helix chain 'A' and resid 2844 through 2858 removed outlier: 3.673A pdb=" N SER A2848 " --> pdb=" O GLY A2844 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A2849 " --> pdb=" O PRO A2845 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A2850 " --> pdb=" O GLU A2846 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A2851 " --> pdb=" O PHE A2847 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A2852 " --> pdb=" O SER A2848 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A2853 " --> pdb=" O ALA A2849 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A2854 " --> pdb=" O SER A2850 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A2855 " --> pdb=" O ILE A2851 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A2856 " --> pdb=" O ILE A2852 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A2857 " --> pdb=" O GLN A2853 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A2858 " --> pdb=" O MET A2854 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2844 through 2858' Processing helix chain 'A' and resid 2867 through 2877 removed outlier: 3.865A pdb=" N CYS A2873 " --> pdb=" O ILE A2869 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A2874 " --> pdb=" O ILE A2870 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A2875 " --> pdb=" O TYR A2871 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A2876 " --> pdb=" O HIS A2872 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A2877 " --> pdb=" O CYS A2873 " (cutoff:3.500A) Processing helix chain 'A' and resid 2877 through 2884 removed outlier: 3.863A pdb=" N LEU A2881 " --> pdb=" O GLY A2877 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A2882 " --> pdb=" O LEU A2878 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A2883 " --> pdb=" O GLU A2879 " (cutoff:3.500A) Processing helix chain 'A' and resid 2888 through 2893 removed outlier: 3.949A pdb=" N GLU A2893 " --> pdb=" O ARG A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2893 through 2901 removed outlier: 3.937A pdb=" N LYS A2897 " --> pdb=" O GLU A2893 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A2898 " --> pdb=" O SER A2894 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A2899 " --> pdb=" O LEU A2895 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A2900 " --> pdb=" O VAL A2896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A2901 " --> pdb=" O LYS A2897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2893 through 2901' Processing helix chain 'A' and resid 2907 through 2925 removed outlier: 3.986A pdb=" N ALA A2913 " --> pdb=" O HIS A2909 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A2914 " --> pdb=" O ARG A2910 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A2915 " --> pdb=" O ALA A2911 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A2916 " --> pdb=" O MET A2912 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A2917 " --> pdb=" O ALA A2913 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A2918 " --> pdb=" O ALA A2914 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A2919 " --> pdb=" O LEU A2915 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A2920 " --> pdb=" O GLY A2916 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A2921 " --> pdb=" O LEU A2917 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A2922 " --> pdb=" O MET A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 2946 through 2963 removed outlier: 3.972A pdb=" N ALA A2950 " --> pdb=" O SER A2946 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A2951 " --> pdb=" O VAL A2947 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU A2952 " --> pdb=" O ILE A2948 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A2953 " --> pdb=" O VAL A2949 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A2954 " --> pdb=" O ALA A2950 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A2955 " --> pdb=" O MET A2951 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A2956 " --> pdb=" O GLU A2952 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A2957 " --> pdb=" O ARG A2953 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A2958 " --> pdb=" O VAL A2954 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A2959 " --> pdb=" O SER A2955 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A2960 " --> pdb=" O VAL A2956 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A2961 " --> pdb=" O LEU A2957 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A2962 " --> pdb=" O PHE A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2968 through 2984 removed outlier: 4.019A pdb=" N VAL A2972 " --> pdb=" O GLU A2968 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A2973 " --> pdb=" O ALA A2969 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A2974 " --> pdb=" O ARG A2970 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A2975 " --> pdb=" O VAL A2971 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A2976 " --> pdb=" O VAL A2972 " (cutoff:3.500A) Proline residue: A2977 - end of helix removed outlier: 3.863A pdb=" N LEU A2980 " --> pdb=" O LEU A2976 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP A2981 " --> pdb=" O PRO A2977 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A2982 " --> pdb=" O GLN A2978 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A2983 " --> pdb=" O PHE A2979 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE A2984 " --> pdb=" O LEU A2980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2968 through 2984' Processing helix chain 'A' and resid 2985 through 2995 removed outlier: 4.464A pdb=" N ASN A2991 " --> pdb=" O GLN A2987 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A2992 " --> pdb=" O ASP A2988 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A2993 " --> pdb=" O ILE A2989 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A2994 " --> pdb=" O MET A2990 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A2995 " --> pdb=" O ASN A2991 " (cutoff:3.500A) Processing helix chain 'A' and resid 3005 through 3017 removed outlier: 3.968A pdb=" N THR A3010 " --> pdb=" O GLN A3006 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A3011 " --> pdb=" O PHE A3007 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A3012 " --> pdb=" O MET A3008 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR A3013 " --> pdb=" O ALA A3009 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A3014 " --> pdb=" O THR A3010 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A3015 " --> pdb=" O VAL A3011 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A3016 " --> pdb=" O VAL A3012 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A3017 " --> pdb=" O TYR A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3038 removed outlier: 3.885A pdb=" N ASP A3030 " --> pdb=" O SER A3026 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP A3031 " --> pdb=" O MET A3027 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A3032 " --> pdb=" O VAL A3028 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET A3033 " --> pdb=" O ARG A3029 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A3034 " --> pdb=" O ASP A3030 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A3035 " --> pdb=" O TRP A3031 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A3036 " --> pdb=" O VAL A3032 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A3037 " --> pdb=" O MET A3033 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN A3038 " --> pdb=" O LEU A3034 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3026 through 3038' Processing helix chain 'A' and resid 3044 through 3059 removed outlier: 3.943A pdb=" N THR A3049 " --> pdb=" O VAL A3045 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A3050 " --> pdb=" O ALA A3046 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A3051 " --> pdb=" O MET A3047 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A3052 " --> pdb=" O ALA A3048 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A3053 " --> pdb=" O THR A3049 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A3054 " --> pdb=" O TRP A3050 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A3055 " --> pdb=" O SER A3051 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A3056 " --> pdb=" O LEU A3052 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A3057 " --> pdb=" O SER A3053 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A3058 " --> pdb=" O CYS A3054 " (cutoff:3.500A) Processing helix chain 'A' and resid 3065 through 3067 No H-bonds generated for 'chain 'A' and resid 3065 through 3067' Processing helix chain 'A' and resid 3068 through 3073 Processing helix chain 'A' and resid 3080 through 3094 removed outlier: 3.747A pdb=" N ASN A3085 " --> pdb=" O GLN A3081 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A3086 " --> pdb=" O VAL A3082 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A3087 " --> pdb=" O ASP A3083 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A3088 " --> pdb=" O VAL A3084 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A3089 " --> pdb=" O ASN A3085 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A3090 " --> pdb=" O LEU A3086 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A3091 " --> pdb=" O PHE A3087 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A3092 " --> pdb=" O CYS A3088 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP A3093 " --> pdb=" O LEU A3089 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A3094 " --> pdb=" O VAL A3090 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 4.007A pdb=" N GLU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 54 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 59' Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.893A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 72 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.933A pdb=" N ALA B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 90' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.823A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.864A pdb=" N LEU B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 149 " --> pdb=" O CYS B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 159 through 171 removed outlier: 4.000A pdb=" N GLY B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 169 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 171' Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.882A pdb=" N GLN B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.852A pdb=" N MET B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 211 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.998A pdb=" N THR B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 297' Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.890A pdb=" N GLN B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.952A pdb=" N LYS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.994A pdb=" N LEU B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 356' Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.862A pdb=" N LEU B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 361 " --> pdb=" O HIS B 357 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 432 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: 3.39 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6653 1.34 - 1.47: 4604 1.47 - 1.59: 9441 1.59 - 1.72: 0 1.72 - 1.84: 187 Bond restraints: 20885 Sorted by residual: bond pdb=" C SER A3062 " pdb=" N PRO A3063 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" CB PRO A1931 " pdb=" CG PRO A1931 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.80e+00 bond pdb=" C ILE A1513 " pdb=" N PRO A1514 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.27e+00 bond pdb=" CB PRO A2513 " pdb=" CG PRO A2513 " ideal model delta sigma weight residual 1.492 1.383 0.109 5.00e-02 4.00e+02 4.79e+00 bond pdb=" C VAL A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.54e+00 ... (remaining 20880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 27702 3.39 - 6.79: 565 6.79 - 10.18: 93 10.18 - 13.57: 13 13.57 - 16.96: 1 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N VAL A1645 " pdb=" CA VAL A1645 " pdb=" C VAL A1645 " ideal model delta sigma weight residual 111.91 105.43 6.48 8.90e-01 1.26e+00 5.30e+01 angle pdb=" N THR A 670 " pdb=" CA THR A 670 " pdb=" C THR A 670 " ideal model delta sigma weight residual 114.75 105.96 8.79 1.26e+00 6.30e-01 4.87e+01 angle pdb=" C VAL A2703 " pdb=" N SER A2704 " pdb=" CA SER A2704 " ideal model delta sigma weight residual 120.60 129.62 -9.02 1.60e+00 3.91e-01 3.18e+01 angle pdb=" N PHE A1259 " pdb=" CA PHE A1259 " pdb=" C PHE A1259 " ideal model delta sigma weight residual 113.43 106.37 7.06 1.26e+00 6.30e-01 3.14e+01 angle pdb=" C LEU A2593 " pdb=" N LEU A2594 " pdb=" CA LEU A2594 " ideal model delta sigma weight residual 120.82 129.00 -8.18 1.50e+00 4.44e-01 2.97e+01 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 11854 16.36 - 32.72: 688 32.72 - 49.08: 115 49.08 - 65.44: 9 65.44 - 81.80: 14 Dihedral angle restraints: 12680 sinusoidal: 5006 harmonic: 7674 Sorted by residual: dihedral pdb=" CA VAL A1045 " pdb=" C VAL A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual -180.00 -105.51 -74.49 0 5.00e+00 4.00e-02 2.22e+02 dihedral pdb=" CA VAL A 296 " pdb=" C VAL A 296 " pdb=" N PRO A 297 " pdb=" CA PRO A 297 " ideal model delta harmonic sigma weight residual -180.00 -123.26 -56.74 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual 180.00 129.69 50.31 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2667 0.067 - 0.133: 631 0.133 - 0.200: 80 0.200 - 0.266: 16 0.266 - 0.333: 1 Chirality restraints: 3395 Sorted by residual: chirality pdb=" CB VAL A 296 " pdb=" CA VAL A 296 " pdb=" CG1 VAL A 296 " pdb=" CG2 VAL A 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU B 108 " pdb=" CB LEU B 108 " pdb=" CD1 LEU B 108 " pdb=" CD2 LEU B 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE A2813 " pdb=" CA ILE A2813 " pdb=" CG1 ILE A2813 " pdb=" CG2 ILE A2813 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3392 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2214 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A2215 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A2215 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A2215 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1045 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A1046 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A1046 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1046 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1930 " -0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A1931 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A1931 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1931 " -0.055 5.00e-02 4.00e+02 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5740 2.80 - 3.33: 17309 3.33 - 3.85: 30707 3.85 - 4.38: 39014 4.38 - 4.90: 63335 Nonbonded interactions: 156105 Sorted by model distance: nonbonded pdb=" O GLU A1749 " pdb=" OG1 THR A1753 " model vdw 2.277 3.040 nonbonded pdb=" O MET A2362 " pdb=" OG SER A2365 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 167 " pdb=" O ASN A 204 " model vdw 2.299 3.040 nonbonded pdb=" O ASN A1245 " pdb=" OG1 THR A1249 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A2455 " pdb=" OE1 GLN A2459 " model vdw 2.309 3.040 ... (remaining 156100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.140 20887 Z= 0.318 Angle : 1.295 16.963 28378 Z= 0.717 Chirality : 0.057 0.333 3395 Planarity : 0.010 0.113 3576 Dihedral : 11.104 77.215 7660 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.14 % Favored : 93.59 % Rotamer: Outliers : 0.83 % Allowed : 5.71 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -5.17 (0.12), residues: 2575 helix: -5.23 (0.04), residues: 1081 sheet: None (None), residues: 0 loop : -1.98 (0.13), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2528 TYR 0.034 0.003 TYR A 167 PHE 0.040 0.003 PHE A 238 TRP 0.029 0.003 TRP A2288 HIS 0.018 0.003 HIS A1940 Details of bonding type rmsd covalent geometry : bond 0.00706 (20885) covalent geometry : angle 1.29466 (28374) SS BOND : bond 0.00738 ( 2) SS BOND : angle 2.86511 ( 4) hydrogen bonds : bond 0.32462 ( 158) hydrogen bonds : angle 11.95807 ( 432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 701 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7770 (mt) cc_final: 0.7306 (mt) REVERT: A 300 ASP cc_start: 0.6468 (m-30) cc_final: 0.6135 (t0) REVERT: A 706 SER cc_start: 0.7837 (p) cc_final: 0.7469 (m) REVERT: A 731 TYR cc_start: 0.8354 (m-80) cc_final: 0.7504 (m-80) REVERT: A 870 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6850 (mt-10) REVERT: A 1355 PHE cc_start: 0.7704 (t80) cc_final: 0.7127 (t80) REVERT: A 1468 ILE cc_start: 0.8857 (tp) cc_final: 0.8653 (tp) REVERT: A 1485 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7964 (mt-10) REVERT: A 1594 GLU cc_start: 0.6192 (tt0) cc_final: 0.5742 (tt0) REVERT: A 1647 MET cc_start: 0.7657 (tpt) cc_final: 0.7450 (tpt) REVERT: A 1670 SER cc_start: 0.9204 (p) cc_final: 0.8733 (t) REVERT: A 1702 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8668 (pt) REVERT: A 1742 GLN cc_start: 0.7412 (tt0) cc_final: 0.6690 (tt0) REVERT: A 1784 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6954 (mtpp) REVERT: A 1828 LEU cc_start: 0.9181 (mt) cc_final: 0.8941 (mp) REVERT: A 1921 GLN cc_start: 0.7339 (mt0) cc_final: 0.6873 (tt0) REVERT: A 1958 GLU cc_start: 0.7802 (pt0) cc_final: 0.6002 (mt-10) REVERT: A 1959 ASN cc_start: 0.7250 (t160) cc_final: 0.6222 (t160) REVERT: A 2185 VAL cc_start: 0.9170 (p) cc_final: 0.8919 (m) REVERT: A 2270 ASP cc_start: 0.6563 (m-30) cc_final: 0.6308 (m-30) REVERT: A 2510 MET cc_start: 0.7831 (tmt) cc_final: 0.7073 (tmm) REVERT: A 2554 ILE cc_start: 0.7978 (mt) cc_final: 0.7641 (tt) REVERT: A 2567 HIS cc_start: 0.7492 (p-80) cc_final: 0.7237 (p-80) REVERT: A 2736 GLN cc_start: 0.7243 (pp30) cc_final: 0.6891 (pp30) REVERT: A 2841 LEU cc_start: 0.8175 (mt) cc_final: 0.7930 (tt) REVERT: A 2869 ILE cc_start: 0.8231 (mt) cc_final: 0.7996 (pt) REVERT: A 2923 TYR cc_start: 0.7438 (m-10) cc_final: 0.7190 (m-80) REVERT: B 138 PRO cc_start: 0.8821 (Cg_endo) cc_final: 0.8512 (Cg_exo) REVERT: B 288 LEU cc_start: 0.8558 (mt) cc_final: 0.8307 (mt) REVERT: B 339 SER cc_start: 0.8434 (m) cc_final: 0.8194 (t) outliers start: 19 outliers final: 3 residues processed: 710 average time/residue: 0.1560 time to fit residues: 169.3308 Evaluate side-chains 453 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 2512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 258 optimal weight: 0.4980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 240 ASN A 254 ASN A 275 GLN A 366 HIS A 377 GLN A 399 GLN ** A 984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 HIS A1146 ASN A1492 ASN A1533 HIS A1589 GLN A1592 HIS A1657 ASN A1764 GLN ** A1765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN A2026 GLN A2103 GLN A2133 ASN A2137 ASN A2234 HIS ** A2236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2367 GLN A2459 GLN A2563 ASN A2612 GLN A2622 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2872 HIS ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.179620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.156327 restraints weight = 26049.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.158329 restraints weight = 17847.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.159133 restraints weight = 14020.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.159597 restraints weight = 11208.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.159913 restraints weight = 10376.188| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20887 Z= 0.112 Angle : 0.693 9.626 28378 Z= 0.344 Chirality : 0.041 0.185 3395 Planarity : 0.006 0.080 3576 Dihedral : 6.869 67.450 2805 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 3.43 % Allowed : 12.74 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.72 (0.13), residues: 2575 helix: -4.77 (0.07), residues: 1194 sheet: None (None), residues: 0 loop : -1.46 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2962 TYR 0.023 0.001 TYR A2675 PHE 0.040 0.001 PHE A 238 TRP 0.022 0.001 TRP A2573 HIS 0.007 0.001 HIS A1940 Details of bonding type rmsd covalent geometry : bond 0.00255 (20885) covalent geometry : angle 0.69337 (28374) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.79955 ( 4) hydrogen bonds : bond 0.04466 ( 158) hydrogen bonds : angle 7.29762 ( 432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 512 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6257 (mmp) cc_final: 0.5825 (ptt) REVERT: A 198 CYS cc_start: 0.8247 (p) cc_final: 0.7853 (p) REVERT: A 241 ASP cc_start: 0.5926 (m-30) cc_final: 0.5424 (m-30) REVERT: A 731 TYR cc_start: 0.8187 (m-80) cc_final: 0.7384 (m-80) REVERT: A 745 TYR cc_start: 0.8721 (m-80) cc_final: 0.8382 (m-80) REVERT: A 994 MET cc_start: 0.8069 (tpp) cc_final: 0.7229 (tpp) REVERT: A 1062 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8302 (ptp) REVERT: A 1084 ASP cc_start: 0.8239 (m-30) cc_final: 0.7746 (t0) REVERT: A 1088 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (tp) REVERT: A 1302 MET cc_start: 0.8550 (tmm) cc_final: 0.8319 (tmm) REVERT: A 1356 MET cc_start: 0.8538 (tpp) cc_final: 0.7900 (tpp) REVERT: A 1443 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: A 1485 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8141 (mt-10) REVERT: A 1501 SER cc_start: 0.8433 (p) cc_final: 0.8142 (p) REVERT: A 1640 SER cc_start: 0.9004 (p) cc_final: 0.8749 (t) REVERT: A 1670 SER cc_start: 0.9157 (p) cc_final: 0.8794 (t) REVERT: A 1743 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7803 (tm) REVERT: A 1763 GLN cc_start: 0.6596 (pm20) cc_final: 0.5975 (pm20) REVERT: A 1775 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 1784 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7410 (mtpp) REVERT: A 1958 GLU cc_start: 0.7811 (pt0) cc_final: 0.7603 (pt0) REVERT: A 1959 ASN cc_start: 0.7424 (t160) cc_final: 0.7049 (t160) REVERT: A 1973 LEU cc_start: 0.8131 (mt) cc_final: 0.7822 (mt) REVERT: A 2103 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 2268 SER cc_start: 0.8390 (t) cc_final: 0.8188 (p) REVERT: A 2272 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 2510 MET cc_start: 0.8031 (tmt) cc_final: 0.6998 (tmt) REVERT: A 2567 HIS cc_start: 0.7351 (p-80) cc_final: 0.7093 (p-80) REVERT: A 2713 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7380 (t80) REVERT: A 2730 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7367 (tt0) REVERT: A 2841 LEU cc_start: 0.8303 (mt) cc_final: 0.8018 (tt) REVERT: A 2854 MET cc_start: 0.7758 (tpp) cc_final: 0.7328 (mmt) REVERT: B 92 GLU cc_start: 0.8368 (tp30) cc_final: 0.8037 (tp30) REVERT: B 286 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8542 (mtpt) REVERT: B 339 SER cc_start: 0.8694 (m) cc_final: 0.8481 (t) outliers start: 78 outliers final: 28 residues processed: 560 average time/residue: 0.1453 time to fit residues: 129.2593 Evaluate side-chains 450 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 415 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1443 GLN Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1812 ASP Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2103 GLN Chi-restraints excluded: chain A residue 2234 HIS Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2522 CYS Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2815 HIS Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 353 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 4 optimal weight: 9.9990 chunk 230 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 157 optimal weight: 0.0070 chunk 254 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A1589 GLN A1742 GLN A1765 HIS A1959 ASN ** A2236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2459 GLN A2622 ASN A2669 GLN A2712 GLN A2872 HIS A2909 HIS ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3071 HIS ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** 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 = 0.3752 r_free = 0.3752 target = 0.172093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.148957 restraints weight = 26455.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.150238 restraints weight = 17731.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.151051 restraints weight = 13533.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.151903 restraints weight = 11535.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.152052 restraints weight = 10115.514| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20887 Z= 0.109 Angle : 0.654 9.804 28378 Z= 0.316 Chirality : 0.041 0.196 3395 Planarity : 0.005 0.072 3576 Dihedral : 6.001 64.135 2800 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 4.13 % Allowed : 13.97 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -4.44 (0.14), residues: 2575 helix: -4.40 (0.08), residues: 1286 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2601 TYR 0.015 0.001 TYR A2211 PHE 0.041 0.001 PHE A 238 TRP 0.023 0.001 TRP B 345 HIS 0.017 0.001 HIS A2234 Details of bonding type rmsd covalent geometry : bond 0.00261 (20885) covalent geometry : angle 0.65409 (28374) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.55359 ( 4) hydrogen bonds : bond 0.03250 ( 158) hydrogen bonds : angle 6.48145 ( 432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 457 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 TYR cc_start: 0.8225 (m-80) cc_final: 0.7453 (m-80) REVERT: A 735 LEU cc_start: 0.7449 (tt) cc_final: 0.7043 (tp) REVERT: A 745 TYR cc_start: 0.8726 (m-80) cc_final: 0.8140 (m-80) REVERT: A 761 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7805 (mtm-85) REVERT: A 813 ASP cc_start: 0.7894 (t70) cc_final: 0.7385 (t70) REVERT: A 1084 ASP cc_start: 0.8423 (m-30) cc_final: 0.7955 (t0) REVERT: A 1355 PHE cc_start: 0.7872 (t80) cc_final: 0.7316 (t80) REVERT: A 1356 MET cc_start: 0.8583 (tpp) cc_final: 0.8006 (tpp) REVERT: A 1595 ASN cc_start: 0.7572 (p0) cc_final: 0.7322 (p0) REVERT: A 1640 SER cc_start: 0.9043 (p) cc_final: 0.8748 (t) REVERT: A 1670 SER cc_start: 0.9199 (p) cc_final: 0.8884 (t) REVERT: A 1742 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8271 (tp-100) REVERT: A 1743 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8090 (tm) REVERT: A 1884 MET cc_start: 0.7921 (ttt) cc_final: 0.7613 (ttt) REVERT: A 2005 ASP cc_start: 0.7352 (t0) cc_final: 0.7030 (t0) REVERT: A 2272 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8160 (tm-30) REVERT: A 2390 ASN cc_start: 0.8928 (t0) cc_final: 0.8464 (t0) REVERT: A 2510 MET cc_start: 0.8018 (tmt) cc_final: 0.6926 (tmt) REVERT: A 2567 HIS cc_start: 0.7246 (p-80) cc_final: 0.6937 (p-80) REVERT: A 2713 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7572 (t80) REVERT: A 2730 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7205 (tt0) REVERT: A 2841 LEU cc_start: 0.8366 (mt) cc_final: 0.8042 (tt) REVERT: A 2854 MET cc_start: 0.8142 (tpp) cc_final: 0.7544 (mmt) REVERT: A 2909 HIS cc_start: 0.6106 (p90) cc_final: 0.5880 (p-80) REVERT: A 2918 MET cc_start: 0.6892 (mmt) cc_final: 0.6533 (mmt) REVERT: B 92 GLU cc_start: 0.8513 (tp30) cc_final: 0.8095 (tp30) REVERT: B 286 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8242 (mtpt) outliers start: 94 outliers final: 47 residues processed: 514 average time/residue: 0.1361 time to fit residues: 112.1123 Evaluate side-chains 461 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 411 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1742 GLN Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1812 ASP Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2522 CYS Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2623 SER Chi-restraints excluded: chain A residue 2669 GLN Chi-restraints excluded: chain A residue 2697 VAL Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2815 HIS Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 253 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 257 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 GLN A1091 ASN A1140 HIS A1150 HIS A1657 ASN A2048 HIS A2103 GLN A2236 HIS A2305 HIS A2459 GLN A2526 GLN A2552 GLN A2712 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3006 GLN ** A3024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3071 HIS ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 357 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.156039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.133688 restraints weight = 26816.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132916 restraints weight = 22081.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134392 restraints weight = 19907.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.135039 restraints weight = 15787.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.135157 restraints weight = 13173.796| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 20887 Z= 0.202 Angle : 0.732 9.704 28378 Z= 0.358 Chirality : 0.045 0.205 3395 Planarity : 0.005 0.072 3576 Dihedral : 6.034 64.499 2800 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 4.96 % Allowed : 15.24 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -4.31 (0.14), residues: 2575 helix: -3.91 (0.09), residues: 1436 sheet: None (None), residues: 0 loop : -1.10 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 194 TYR 0.020 0.002 TYR A2211 PHE 0.028 0.002 PHE A 238 TRP 0.021 0.002 TRP B 345 HIS 0.009 0.001 HIS A2259 Details of bonding type rmsd covalent geometry : bond 0.00485 (20885) covalent geometry : angle 0.73233 (28374) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.78558 ( 4) hydrogen bonds : bond 0.03619 ( 158) hydrogen bonds : angle 6.37731 ( 432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 471 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 205 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7583 (tp) REVERT: A 731 TYR cc_start: 0.8374 (m-80) cc_final: 0.7636 (m-80) REVERT: A 745 TYR cc_start: 0.8814 (m-80) cc_final: 0.8423 (m-80) REVERT: A 791 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7826 (mmm-85) REVERT: A 813 ASP cc_start: 0.7980 (t70) cc_final: 0.7776 (t70) REVERT: A 826 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (t) REVERT: A 835 SER cc_start: 0.8667 (p) cc_final: 0.8463 (p) REVERT: A 940 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6566 (mm-40) REVERT: A 953 GLN cc_start: 0.8306 (tt0) cc_final: 0.8095 (tt0) REVERT: A 1062 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8249 (ptp) REVERT: A 1084 ASP cc_start: 0.8449 (m-30) cc_final: 0.8214 (t0) REVERT: A 1235 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7626 (tp) REVERT: A 1584 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: A 1640 SER cc_start: 0.9024 (p) cc_final: 0.8722 (t) REVERT: A 1670 SER cc_start: 0.9262 (p) cc_final: 0.9051 (t) REVERT: A 1743 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8497 (tm) REVERT: A 1905 ASN cc_start: 0.8992 (p0) cc_final: 0.8491 (p0) REVERT: A 2005 ASP cc_start: 0.7323 (t0) cc_final: 0.7078 (t0) REVERT: A 2117 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 2135 GLU cc_start: 0.6052 (tt0) cc_final: 0.5406 (pm20) REVERT: A 2272 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 2304 ILE cc_start: 0.9337 (mm) cc_final: 0.9056 (mt) REVERT: A 2424 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 2510 MET cc_start: 0.8172 (tmt) cc_final: 0.7067 (tmt) REVERT: A 2532 LEU cc_start: 0.7071 (mt) cc_final: 0.6786 (mt) REVERT: A 2695 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 2713 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (t80) REVERT: A 2730 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7247 (tt0) REVERT: A 2737 TYR cc_start: 0.8083 (m-80) cc_final: 0.7444 (m-80) REVERT: A 2841 LEU cc_start: 0.8372 (mt) cc_final: 0.8133 (tt) REVERT: A 2854 MET cc_start: 0.8692 (tpp) cc_final: 0.8014 (mmt) REVERT: A 2912 MET cc_start: 0.9250 (mmt) cc_final: 0.9036 (tpp) REVERT: B 92 GLU cc_start: 0.8535 (tp30) cc_final: 0.8249 (tp30) REVERT: B 153 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.8566 (ttp-110) REVERT: B 167 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7996 (ttt-90) REVERT: B 343 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7260 (mt-10) outliers start: 113 outliers final: 64 residues processed: 540 average time/residue: 0.1512 time to fit residues: 126.3455 Evaluate side-chains 482 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 410 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2022 SER Chi-restraints excluded: chain A residue 2217 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2424 PHE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2522 CYS Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2614 SER Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2697 VAL Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2827 VAL Chi-restraints excluded: chain A residue 2955 SER Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 337 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 135 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A1091 ASN A1852 GLN A2048 HIS A2103 GLN A2612 GLN A2669 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.128943 restraints weight = 26798.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.128617 restraints weight = 24242.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.129479 restraints weight = 20144.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.129861 restraints weight = 17127.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.130201 restraints weight = 15032.526| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20887 Z= 0.166 Angle : 0.675 11.236 28378 Z= 0.327 Chirality : 0.044 0.222 3395 Planarity : 0.005 0.070 3576 Dihedral : 5.861 64.248 2800 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.03 % Rotamer: Outliers : 4.57 % Allowed : 17.65 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.88 (0.15), residues: 2575 helix: -3.41 (0.10), residues: 1474 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2219 TYR 0.013 0.001 TYR A2211 PHE 0.019 0.002 PHE A2383 TRP 0.017 0.001 TRP A2573 HIS 0.009 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00405 (20885) covalent geometry : angle 0.67516 (28374) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.78146 ( 4) hydrogen bonds : bond 0.03142 ( 158) hydrogen bonds : angle 6.14601 ( 432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 437 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 731 TYR cc_start: 0.8322 (m-80) cc_final: 0.7558 (m-80) REVERT: A 735 LEU cc_start: 0.7454 (tt) cc_final: 0.6970 (tp) REVERT: A 745 TYR cc_start: 0.8825 (m-80) cc_final: 0.8412 (m-80) REVERT: A 767 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8264 (tt) REVERT: A 791 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7735 (mmm-85) REVERT: A 826 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8717 (t) REVERT: A 835 SER cc_start: 0.8709 (p) cc_final: 0.8354 (p) REVERT: A 930 LEU cc_start: 0.9117 (mt) cc_final: 0.8724 (mt) REVERT: A 1084 ASP cc_start: 0.8461 (m-30) cc_final: 0.8217 (t0) REVERT: A 1235 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7432 (tp) REVERT: A 1271 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8113 (m) REVERT: A 1355 PHE cc_start: 0.7902 (t80) cc_final: 0.7309 (t80) REVERT: A 1640 SER cc_start: 0.8988 (p) cc_final: 0.8757 (t) REVERT: A 1743 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8454 (tm) REVERT: A 1884 MET cc_start: 0.8071 (ttt) cc_final: 0.7747 (ttt) REVERT: A 1905 ASN cc_start: 0.8977 (p0) cc_final: 0.8485 (p0) REVERT: A 1948 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 2005 ASP cc_start: 0.7423 (t0) cc_final: 0.7183 (t0) REVERT: A 2304 ILE cc_start: 0.9281 (mm) cc_final: 0.9031 (mt) REVERT: A 2462 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7112 (mp0) REVERT: A 2510 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7586 (tmt) REVERT: A 2532 LEU cc_start: 0.7184 (mt) cc_final: 0.6916 (mt) REVERT: A 2570 TYR cc_start: 0.4862 (m-80) cc_final: 0.4271 (m-80) REVERT: A 2674 LEU cc_start: 0.8928 (mt) cc_final: 0.8648 (tp) REVERT: A 2706 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 2713 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 2730 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7310 (tt0) REVERT: A 2737 TYR cc_start: 0.8092 (m-80) cc_final: 0.7478 (m-80) REVERT: A 2841 LEU cc_start: 0.8450 (mt) cc_final: 0.8117 (tt) REVERT: A 2854 MET cc_start: 0.8742 (tpp) cc_final: 0.7902 (mmt) REVERT: B 92 GLU cc_start: 0.8564 (tp30) cc_final: 0.8240 (tp30) REVERT: B 153 ARG cc_start: 0.8730 (ttp-110) cc_final: 0.8492 (ttp-110) outliers start: 104 outliers final: 63 residues processed: 506 average time/residue: 0.1448 time to fit residues: 115.3182 Evaluate side-chains 471 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 399 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 984 ASN Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2022 SER Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2217 LEU Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2697 VAL Chi-restraints excluded: chain A residue 2706 LEU Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2802 ILE Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 295 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 60 optimal weight: 0.4980 chunk 222 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 204 optimal weight: 0.0770 chunk 5 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 240 ASN A 242 ASN A 302 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 ASN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS A2234 HIS A2669 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.157637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.134798 restraints weight = 25713.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.134990 restraints weight = 24682.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.136047 restraints weight = 21339.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.137023 restraints weight = 16598.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.137086 restraints weight = 14221.401| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20887 Z= 0.104 Angle : 0.639 11.995 28378 Z= 0.303 Chirality : 0.040 0.241 3395 Planarity : 0.004 0.066 3576 Dihedral : 5.395 61.391 2800 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.47 % Allowed : 19.85 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.46 (0.15), residues: 2575 helix: -2.97 (0.11), residues: 1493 sheet: None (None), residues: 0 loop : -0.96 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 761 TYR 0.011 0.001 TYR A2839 PHE 0.029 0.001 PHE A2205 TRP 0.011 0.001 TRP A2454 HIS 0.010 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00253 (20885) covalent geometry : angle 0.63904 (28374) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.79767 ( 4) hydrogen bonds : bond 0.02607 ( 158) hydrogen bonds : angle 5.94631 ( 432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 451 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7777 (tp) REVERT: A 350 LEU cc_start: 0.8757 (mt) cc_final: 0.8512 (mp) REVERT: A 731 TYR cc_start: 0.8232 (m-80) cc_final: 0.7441 (m-80) REVERT: A 735 LEU cc_start: 0.7551 (tt) cc_final: 0.7146 (tp) REVERT: A 744 GLN cc_start: 0.8487 (pm20) cc_final: 0.7417 (pt0) REVERT: A 745 TYR cc_start: 0.8717 (m-80) cc_final: 0.8373 (m-80) REVERT: A 767 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 791 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7660 (mmm-85) REVERT: A 826 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8662 (t) REVERT: A 930 LEU cc_start: 0.9013 (mt) cc_final: 0.8652 (mt) REVERT: A 953 GLN cc_start: 0.8384 (tt0) cc_final: 0.8166 (tt0) REVERT: A 1102 ARG cc_start: 0.4464 (mmt180) cc_final: 0.4196 (mpt180) REVERT: A 1355 PHE cc_start: 0.7880 (t80) cc_final: 0.7261 (t80) REVERT: A 1652 MET cc_start: 0.7559 (ttt) cc_final: 0.7184 (ttt) REVERT: A 1743 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8427 (tm) REVERT: A 1905 ASN cc_start: 0.8923 (p0) cc_final: 0.8397 (p0) REVERT: A 1948 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 2005 ASP cc_start: 0.7263 (t0) cc_final: 0.7061 (t0) REVERT: A 2010 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6384 (mtp180) REVERT: A 2024 MET cc_start: 0.7727 (mmm) cc_final: 0.7149 (mmm) REVERT: A 2103 GLN cc_start: 0.8540 (mp10) cc_final: 0.8142 (mp10) REVERT: A 2136 PHE cc_start: 0.8832 (t80) cc_final: 0.8595 (t80) REVERT: A 2304 ILE cc_start: 0.9272 (mm) cc_final: 0.9009 (mt) REVERT: A 2510 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7326 (tmt) REVERT: A 2570 TYR cc_start: 0.4905 (m-80) cc_final: 0.4314 (m-80) REVERT: A 2674 LEU cc_start: 0.8891 (mt) cc_final: 0.8577 (tp) REVERT: A 2710 ARG cc_start: 0.7622 (tpt90) cc_final: 0.7287 (tpt90) REVERT: A 2730 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7368 (tt0) REVERT: A 2737 TYR cc_start: 0.8116 (m-80) cc_final: 0.7500 (m-80) REVERT: A 2839 TYR cc_start: 0.6975 (m-80) cc_final: 0.6658 (m-80) REVERT: A 2841 LEU cc_start: 0.8383 (mt) cc_final: 0.8092 (tt) REVERT: A 2854 MET cc_start: 0.8672 (tpp) cc_final: 0.8265 (mmt) REVERT: B 92 GLU cc_start: 0.8478 (tp30) cc_final: 0.8152 (tp30) outliers start: 79 outliers final: 49 residues processed: 495 average time/residue: 0.1436 time to fit residues: 111.1707 Evaluate side-chains 461 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 406 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2615 ILE Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2802 ILE Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 323 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 399 GLN A1533 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 HIS ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2590 HIS ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.152965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.130134 restraints weight = 26158.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.130461 restraints weight = 23866.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130783 restraints weight = 22624.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.132061 restraints weight = 18628.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.132141 restraints weight = 15146.366| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20887 Z= 0.158 Angle : 0.668 13.678 28378 Z= 0.318 Chirality : 0.043 0.242 3395 Planarity : 0.004 0.068 3576 Dihedral : 5.435 62.154 2800 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 3.78 % Allowed : 20.29 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.27 (0.15), residues: 2575 helix: -2.65 (0.11), residues: 1531 sheet: None (None), residues: 0 loop : -1.07 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2457 TYR 0.012 0.001 TYR A2675 PHE 0.024 0.002 PHE A2205 TRP 0.012 0.001 TRP A2573 HIS 0.009 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00390 (20885) covalent geometry : angle 0.66753 (28374) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.93889 ( 4) hydrogen bonds : bond 0.02947 ( 158) hydrogen bonds : angle 6.00619 ( 432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 731 TYR cc_start: 0.8298 (m-80) cc_final: 0.7494 (m-80) REVERT: A 735 LEU cc_start: 0.7800 (tt) cc_final: 0.7385 (tp) REVERT: A 744 GLN cc_start: 0.8501 (pm20) cc_final: 0.7611 (pt0) REVERT: A 745 TYR cc_start: 0.8772 (m-80) cc_final: 0.8356 (m-80) REVERT: A 767 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 771 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 1084 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8478 (t0) REVERT: A 1102 ARG cc_start: 0.3958 (mmt180) cc_final: 0.3748 (mpt180) REVERT: A 1355 PHE cc_start: 0.7951 (t80) cc_final: 0.7257 (t80) REVERT: A 1652 MET cc_start: 0.7855 (ttt) cc_final: 0.7520 (ttt) REVERT: A 1733 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7493 (pt0) REVERT: A 1743 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8458 (tm) REVERT: A 1905 ASN cc_start: 0.8929 (p0) cc_final: 0.8470 (p0) REVERT: A 1921 GLN cc_start: 0.7679 (mt0) cc_final: 0.6814 (tt0) REVERT: A 1948 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 1965 MET cc_start: 0.9042 (tpp) cc_final: 0.8740 (tpp) REVERT: A 2005 ASP cc_start: 0.7418 (t0) cc_final: 0.7167 (t0) REVERT: A 2024 MET cc_start: 0.7705 (mmm) cc_final: 0.7234 (mmm) REVERT: A 2103 GLN cc_start: 0.8633 (mp10) cc_final: 0.8209 (mp10) REVERT: A 2136 PHE cc_start: 0.8929 (t80) cc_final: 0.8596 (t80) REVERT: A 2304 ILE cc_start: 0.9278 (mm) cc_final: 0.9050 (mt) REVERT: A 2454 TRP cc_start: 0.8319 (OUTLIER) cc_final: 0.7745 (p-90) REVERT: A 2462 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7455 (mp0) REVERT: A 2570 TYR cc_start: 0.4973 (m-80) cc_final: 0.4438 (m-80) REVERT: A 2710 ARG cc_start: 0.7536 (tpt90) cc_final: 0.7282 (tpt90) REVERT: A 2713 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8563 (t80) REVERT: A 2730 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7335 (tt0) REVERT: A 2737 TYR cc_start: 0.8216 (m-80) cc_final: 0.7627 (m-80) REVERT: A 2841 LEU cc_start: 0.8393 (mt) cc_final: 0.8044 (tt) REVERT: A 2854 MET cc_start: 0.8683 (tpp) cc_final: 0.8279 (mmt) REVERT: B 92 GLU cc_start: 0.8538 (tp30) cc_final: 0.8228 (tp30) REVERT: B 186 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6837 (mt-10) outliers start: 86 outliers final: 61 residues processed: 480 average time/residue: 0.1423 time to fit residues: 107.9653 Evaluate side-chains 469 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 400 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 CYS Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1436 THR Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1501 SER Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1906 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2217 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2454 TRP Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2573 TRP Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2802 ILE Chi-restraints excluded: chain A residue 2976 LEU Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3012 VAL Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 295 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 114 optimal weight: 0.0000 chunk 111 optimal weight: 0.0770 chunk 259 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1730 ASN A1852 GLN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2563 ASN A2568 HIS ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3085 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.134745 restraints weight = 25990.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.135864 restraints weight = 22820.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.136717 restraints weight = 18485.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.137346 restraints weight = 15270.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.137499 restraints weight = 13327.707| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20887 Z= 0.098 Angle : 0.636 12.982 28378 Z= 0.300 Chirality : 0.040 0.263 3395 Planarity : 0.004 0.064 3576 Dihedral : 4.914 58.534 2798 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.72 % Allowed : 21.96 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % 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 aren not related in a simple way. whole: -2.77 (0.16), residues: 2575 helix: -2.27 (0.12), residues: 1524 sheet: None (None), residues: 0 loop : -0.84 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1941 TYR 0.010 0.001 TYR B 114 PHE 0.022 0.001 PHE A2205 TRP 0.011 0.001 TRP A2573 HIS 0.008 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00233 (20885) covalent geometry : angle 0.63611 (28374) SS BOND : bond 0.00219 ( 2) SS BOND : angle 0.73174 ( 4) hydrogen bonds : bond 0.02355 ( 158) hydrogen bonds : angle 5.77281 ( 432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 416 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.6228 (t0) cc_final: 0.6018 (t0) REVERT: A 663 LYS cc_start: 0.5176 (tptp) cc_final: 0.4838 (tptt) REVERT: A 735 LEU cc_start: 0.7527 (tt) cc_final: 0.7270 (tp) REVERT: A 744 GLN cc_start: 0.8488 (pm20) cc_final: 0.7500 (pt0) REVERT: A 745 TYR cc_start: 0.8652 (m-80) cc_final: 0.8256 (m-80) REVERT: A 767 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 771 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8867 (tp) REVERT: A 850 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8275 (mm) REVERT: A 930 LEU cc_start: 0.8995 (mt) cc_final: 0.8674 (mt) REVERT: A 1084 ASP cc_start: 0.8776 (t0) cc_final: 0.8563 (t0) REVERT: A 1501 SER cc_start: 0.8776 (p) cc_final: 0.8502 (t) REVERT: A 1533 HIS cc_start: 0.8831 (m90) cc_final: 0.8577 (m90) REVERT: A 1652 MET cc_start: 0.7965 (ttt) cc_final: 0.7707 (ttt) REVERT: A 1733 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7595 (pt0) REVERT: A 1743 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8452 (tm) REVERT: A 1905 ASN cc_start: 0.8923 (p0) cc_final: 0.8464 (p0) REVERT: A 1948 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (tt) REVERT: A 1965 MET cc_start: 0.9024 (tpp) cc_final: 0.8613 (tpp) REVERT: A 2010 ARG cc_start: 0.6816 (mtt180) cc_final: 0.6198 (mtp180) REVERT: A 2103 GLN cc_start: 0.8654 (mp10) cc_final: 0.8255 (mp10) REVERT: A 2136 PHE cc_start: 0.8956 (t80) cc_final: 0.8691 (t80) REVERT: A 2454 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7536 (p-90) REVERT: A 2462 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7451 (mp0) REVERT: A 2570 TYR cc_start: 0.4930 (m-80) cc_final: 0.4395 (m-80) REVERT: A 2674 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8628 (tp) REVERT: A 2708 THR cc_start: 0.8661 (p) cc_final: 0.8373 (t) REVERT: A 2730 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7229 (tt0) REVERT: A 2737 TYR cc_start: 0.8175 (m-80) cc_final: 0.7772 (m-80) REVERT: A 2841 LEU cc_start: 0.8271 (mt) cc_final: 0.7914 (tt) REVERT: A 2854 MET cc_start: 0.8714 (tpp) cc_final: 0.8303 (mmt) REVERT: B 186 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6890 (mt-10) REVERT: B 322 LEU cc_start: 0.9112 (mt) cc_final: 0.8906 (tp) outliers start: 62 outliers final: 36 residues processed: 457 average time/residue: 0.1418 time to fit residues: 102.0425 Evaluate side-chains 437 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2454 TRP Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2573 TRP Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2802 ILE Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3051 SER Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 236 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 230 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1730 ASN A1852 GLN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 HIS A2048 HIS ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2820 HIS ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.158947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.135021 restraints weight = 25652.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.135769 restraints weight = 22981.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137202 restraints weight = 18399.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.137616 restraints weight = 15451.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.137901 restraints weight = 13823.552| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20887 Z= 0.098 Angle : 0.622 14.509 28378 Z= 0.293 Chirality : 0.040 0.285 3395 Planarity : 0.004 0.064 3576 Dihedral : 4.733 57.201 2798 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.42 % Allowed : 22.13 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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 aren not related in a simple way. whole: -2.46 (0.16), residues: 2575 helix: -1.95 (0.12), residues: 1519 sheet: None (None), residues: 0 loop : -0.84 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2457 TYR 0.010 0.001 TYR B 114 PHE 0.025 0.001 PHE A2309 TRP 0.010 0.001 TRP A2454 HIS 0.009 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00236 (20885) covalent geometry : angle 0.62159 (28374) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.79325 ( 4) hydrogen bonds : bond 0.02334 ( 158) hydrogen bonds : angle 5.62156 ( 432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 427 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.5143 (tptp) cc_final: 0.4845 (tptt) REVERT: A 735 LEU cc_start: 0.7527 (tt) cc_final: 0.7274 (tp) REVERT: A 744 GLN cc_start: 0.8442 (pm20) cc_final: 0.7530 (pt0) REVERT: A 745 TYR cc_start: 0.8566 (m-80) cc_final: 0.8151 (m-80) REVERT: A 767 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 771 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8856 (tp) REVERT: A 930 LEU cc_start: 0.9059 (mt) cc_final: 0.8707 (mt) REVERT: A 983 TYR cc_start: 0.7163 (p90) cc_final: 0.5526 (p90) REVERT: A 1152 LEU cc_start: 0.8987 (mt) cc_final: 0.8710 (mp) REVERT: A 1533 HIS cc_start: 0.8856 (m90) cc_final: 0.8369 (m-70) REVERT: A 1652 MET cc_start: 0.7902 (ttt) cc_final: 0.7655 (ttt) REVERT: A 1733 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7565 (pt0) REVERT: A 1743 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8412 (tm) REVERT: A 1905 ASN cc_start: 0.8926 (p0) cc_final: 0.8466 (p0) REVERT: A 1948 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8108 (tt) REVERT: A 2024 MET cc_start: 0.7823 (mmm) cc_final: 0.7205 (mmm) REVERT: A 2103 GLN cc_start: 0.8658 (mp10) cc_final: 0.8317 (mp10) REVERT: A 2136 PHE cc_start: 0.8897 (t80) cc_final: 0.8683 (t80) REVERT: A 2211 TYR cc_start: 0.8663 (t80) cc_final: 0.8441 (t80) REVERT: A 2271 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 2454 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7603 (p-90) REVERT: A 2462 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7460 (mp0) REVERT: A 2510 MET cc_start: 0.8213 (tmm) cc_final: 0.7828 (tmm) REVERT: A 2570 TYR cc_start: 0.5260 (m-80) cc_final: 0.4704 (m-80) REVERT: A 2623 SER cc_start: 0.7316 (m) cc_final: 0.7088 (t) REVERT: A 2674 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8622 (tp) REVERT: A 2713 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8408 (t80) REVERT: A 2730 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7181 (tt0) REVERT: A 2737 TYR cc_start: 0.8141 (m-80) cc_final: 0.7767 (m-80) REVERT: A 2841 LEU cc_start: 0.8183 (mt) cc_final: 0.7933 (tt) REVERT: A 2854 MET cc_start: 0.8649 (tpp) cc_final: 0.8314 (mmt) REVERT: A 3055 PHE cc_start: 0.8329 (t80) cc_final: 0.8116 (t80) REVERT: B 92 GLU cc_start: 0.8379 (tp30) cc_final: 0.8060 (tp30) REVERT: B 322 LEU cc_start: 0.9048 (mt) cc_final: 0.8695 (tp) REVERT: B 343 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7136 (mt-10) outliers start: 55 outliers final: 39 residues processed: 461 average time/residue: 0.1372 time to fit residues: 100.5937 Evaluate side-chains 453 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 406 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1680 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2454 TRP Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2573 TRP Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2715 LEU Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 224 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 0.0040 chunk 197 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 HIS A1730 ASN A1770 GLN A1852 GLN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 HIS A2048 HIS ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.159816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.136085 restraints weight = 26537.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.135544 restraints weight = 21928.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.136885 restraints weight = 18621.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.137153 restraints weight = 15929.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137527 restraints weight = 13634.683| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20887 Z= 0.099 Angle : 0.624 14.011 28378 Z= 0.293 Chirality : 0.039 0.272 3395 Planarity : 0.004 0.062 3576 Dihedral : 4.596 55.890 2798 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.42 % Allowed : 22.44 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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 aren not related in a simple way. whole: -2.13 (0.16), residues: 2575 helix: -1.66 (0.13), residues: 1514 sheet: None (None), residues: 0 loop : -0.75 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2457 TYR 0.016 0.001 TYR A2351 PHE 0.022 0.001 PHE A2309 TRP 0.010 0.001 TRP A2454 HIS 0.009 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00237 (20885) covalent geometry : angle 0.62409 (28374) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.76878 ( 4) hydrogen bonds : bond 0.02280 ( 158) hydrogen bonds : angle 5.52193 ( 432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 422 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 663 LYS cc_start: 0.5193 (tptp) cc_final: 0.4872 (tptt) REVERT: A 744 GLN cc_start: 0.8437 (pm20) cc_final: 0.7454 (pt0) REVERT: A 745 TYR cc_start: 0.8476 (m-80) cc_final: 0.8046 (m-80) REVERT: A 767 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 771 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (tp) REVERT: A 796 ASN cc_start: 0.8035 (p0) cc_final: 0.7784 (p0) REVERT: A 829 CYS cc_start: 0.8848 (t) cc_final: 0.8466 (t) REVERT: A 850 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 983 TYR cc_start: 0.7097 (p90) cc_final: 0.5475 (p90) REVERT: A 1084 ASP cc_start: 0.8832 (t0) cc_final: 0.8617 (t0) REVERT: A 1152 LEU cc_start: 0.8914 (mt) cc_final: 0.8643 (mp) REVERT: A 1284 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8491 (mmtp) REVERT: A 1533 HIS cc_start: 0.8863 (m90) cc_final: 0.8420 (m-70) REVERT: A 1652 MET cc_start: 0.7873 (ttt) cc_final: 0.7644 (ttt) REVERT: A 1733 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7673 (pt0) REVERT: A 1755 GLN cc_start: 0.7861 (tp40) cc_final: 0.7655 (tt0) REVERT: A 1884 MET cc_start: 0.8051 (tpp) cc_final: 0.7805 (tpp) REVERT: A 1905 ASN cc_start: 0.8929 (p0) cc_final: 0.8505 (p0) REVERT: A 1921 GLN cc_start: 0.7726 (mt0) cc_final: 0.7123 (mt0) REVERT: A 1948 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8103 (tt) REVERT: A 2024 MET cc_start: 0.8047 (mmm) cc_final: 0.7536 (mmm) REVERT: A 2103 GLN cc_start: 0.8704 (mp10) cc_final: 0.8295 (mp10) REVERT: A 2211 TYR cc_start: 0.8585 (t80) cc_final: 0.8348 (t80) REVERT: A 2271 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 2454 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.7721 (p-90) REVERT: A 2462 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7403 (mp0) REVERT: A 2510 MET cc_start: 0.8168 (tmm) cc_final: 0.7888 (tmm) REVERT: A 2570 TYR cc_start: 0.5316 (m-80) cc_final: 0.4848 (m-80) REVERT: A 2623 SER cc_start: 0.7396 (m) cc_final: 0.7165 (t) REVERT: A 2674 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 2713 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8423 (t80) REVERT: A 2730 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7132 (tt0) REVERT: A 2737 TYR cc_start: 0.8144 (m-80) cc_final: 0.7902 (m-80) REVERT: A 2854 MET cc_start: 0.8659 (tpp) cc_final: 0.8204 (mmt) REVERT: A 3055 PHE cc_start: 0.8373 (t80) cc_final: 0.8169 (t80) REVERT: B 92 GLU cc_start: 0.8381 (tp30) cc_final: 0.8083 (tp30) REVERT: B 322 LEU cc_start: 0.8983 (mt) cc_final: 0.8598 (tp) outliers start: 55 outliers final: 37 residues processed: 456 average time/residue: 0.1413 time to fit residues: 102.3340 Evaluate side-chains 447 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 402 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1139 SER Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1680 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2454 TRP Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 248 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 159 optimal weight: 0.0270 chunk 136 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 180 optimal weight: 0.0170 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1730 ASN A1852 GLN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 HIS A2048 HIS ** A2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2563 ASN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.162904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.139092 restraints weight = 26451.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.138656 restraints weight = 21321.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.139287 restraints weight = 19385.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139839 restraints weight = 16559.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.140078 restraints weight = 14661.526| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20887 Z= 0.094 Angle : 0.628 14.658 28378 Z= 0.290 Chirality : 0.039 0.260 3395 Planarity : 0.004 0.060 3576 Dihedral : 4.423 53.822 2798 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.28 % Allowed : 22.84 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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 aren not related in a simple way. whole: -1.84 (0.16), residues: 2575 helix: -1.37 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.74 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2457 TYR 0.016 0.001 TYR A2351 PHE 0.021 0.001 PHE B 81 TRP 0.037 0.001 TRP A1041 HIS 0.009 0.001 HIS A2567 Details of bonding type rmsd covalent geometry : bond 0.00221 (20885) covalent geometry : angle 0.62810 (28374) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.69997 ( 4) hydrogen bonds : bond 0.02162 ( 158) hydrogen bonds : angle 5.45517 ( 432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.18 seconds wall clock time: 57 minutes 23.40 seconds (3443.40 seconds total)