Starting phenix.real_space_refine on Sun Feb 18 02:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_3984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_3984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_3984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_3984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ez8_3984/02_2024/6ez8_3984.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 981": "NH1" <-> "NH2" Residue "A ARG 1573": "NH1" <-> "NH2" Residue "A ARG 1604": "NH1" <-> "NH2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A ARG 1691": "NH1" <-> "NH2" Residue "A ARG 1709": "NH1" <-> "NH2" Residue "A ARG 1738": "NH1" <-> "NH2" Residue "A ARG 1789": "NH1" <-> "NH2" Residue "A ARG 1800": "NH1" <-> "NH2" Residue "A ARG 1817": "NH1" <-> "NH2" Residue "A ARG 1891": "NH1" <-> "NH2" Residue "A ARG 1991": "NH1" <-> "NH2" Residue "A ARG 1998": "NH1" <-> "NH2" Residue "A ARG 2011": "NH1" <-> "NH2" Residue "A ARG 2059": "NH1" <-> "NH2" Residue "A TYR 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2389": "NH1" <-> "NH2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "A ARG 2457": "NH1" <-> "NH2" Residue "A ARG 2547": "NH1" <-> "NH2" Residue "A ARG 2698": "NH1" <-> "NH2" Residue "A ARG 2902": "NH1" <-> "NH2" Residue "A ARG 2910": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 10.92, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.68 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 3.26 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: 7.21 Time building geometry restraints manager: 8.34 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: 97.39 - 104.84: 417 104.84 - 112.29: 10620 112.29 - 119.74: 7771 119.74 - 127.19: 9307 127.19 - 134.64: 259 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 2.440 nonbonded pdb=" O MET A2362 " pdb=" OG SER A2365 " model vdw 2.298 2.440 nonbonded pdb=" OH TYR A 167 " pdb=" O ASN A 204 " model vdw 2.299 2.440 nonbonded pdb=" O ASN A1245 " pdb=" OG1 THR A1249 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A2455 " pdb=" OE1 GLN A2459 " model vdw 2.309 2.440 ... (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 ========== 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.330 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 54.870 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.380 ------------------------------------------------------------------------------- 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 20885 Z= 0.461 Angle : 1.295 16.963 28374 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP A2288 HIS 0.018 0.003 HIS A1940 PHE 0.040 0.003 PHE A 238 TYR 0.034 0.003 TYR A 167 ARG 0.010 0.001 ARG A2528 *********************** 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 fitting. rotamer outliers: 19 poor density : 701 time to evaluate : 2.300 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: 0.3559 time to fit residues: 388.9187 Evaluate side-chains 453 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 2.464 ------------------------------------------------------------------------------- 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 220 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 275 GLN A 366 HIS A 377 GLN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A1042 HIS A1091 ASN ** A1272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 ASN A1533 HIS A1589 GLN A1592 HIS A1657 ASN ** A1682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1764 GLN ** A1765 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2612 GLN A2622 ASN A2872 HIS ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3017 GLN ** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20885 Z= 0.232 Angle : 0.711 9.683 28374 Z= 0.353 Chirality : 0.043 0.266 3395 Planarity : 0.006 0.082 3576 Dihedral : 7.003 68.139 2805 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 4.04 % Allowed : 12.43 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.13), residues: 2575 helix: -4.77 (0.06), residues: 1263 sheet: None (None), residues: 0 loop : -1.49 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2573 HIS 0.007 0.001 HIS A1940 PHE 0.044 0.002 PHE A 238 TYR 0.023 0.002 TYR A2675 ARG 0.007 0.000 ARG A 177 *********************** 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 598 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 506 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASN cc_start: 0.7362 (t0) cc_final: 0.6912 (t0) REVERT: A 243 GLU cc_start: 0.6665 (mp0) cc_final: 0.5693 (mp0) REVERT: A 731 TYR cc_start: 0.8243 (m-80) cc_final: 0.7547 (m-80) REVERT: A 745 TYR cc_start: 0.8874 (m-80) cc_final: 0.8381 (m-80) REVERT: A 859 LEU cc_start: 0.9062 (mt) cc_final: 0.8255 (tt) REVERT: A 984 ASN cc_start: 0.7677 (t0) cc_final: 0.7373 (t0) REVERT: A 994 MET cc_start: 0.8444 (tpp) cc_final: 0.7425 (tpp) REVERT: A 1062 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8400 (ptp) REVERT: A 1084 ASP cc_start: 0.8413 (m-30) cc_final: 0.7903 (t0) REVERT: A 1088 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 1355 PHE cc_start: 0.7793 (t80) cc_final: 0.7204 (t80) REVERT: A 1356 MET cc_start: 0.8254 (tpp) cc_final: 0.7578 (tpp) REVERT: A 1485 GLU cc_start: 0.8279 (mm-30) cc_final: 0.8071 (mt-10) REVERT: A 1501 SER cc_start: 0.8506 (p) cc_final: 0.8204 (p) REVERT: A 1640 SER cc_start: 0.8973 (p) cc_final: 0.8621 (t) REVERT: A 1647 MET cc_start: 0.7700 (tpt) cc_final: 0.7468 (tpt) REVERT: A 1670 SER cc_start: 0.9196 (p) cc_final: 0.8785 (t) REVERT: A 1702 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8477 (pt) REVERT: A 1742 GLN cc_start: 0.7524 (tt0) cc_final: 0.6902 (tt0) REVERT: A 1743 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8189 (tm) REVERT: A 1923 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7951 (tm) REVERT: A 1959 ASN cc_start: 0.7146 (t160) cc_final: 0.6712 (t160) REVERT: A 2103 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: A 2135 GLU cc_start: 0.5996 (tt0) cc_final: 0.5578 (pm20) REVERT: A 2272 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8245 (tm-30) REVERT: A 2510 MET cc_start: 0.7782 (tmt) cc_final: 0.6814 (tmt) REVERT: A 2564 ILE cc_start: 0.9199 (mm) cc_final: 0.8901 (mt) REVERT: A 2567 HIS cc_start: 0.7364 (p-80) cc_final: 0.7129 (p-80) REVERT: A 2695 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 2713 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7658 (t80) REVERT: A 2730 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7420 (tt0) REVERT: A 2876 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7455 (ttm170) REVERT: B 92 GLU cc_start: 0.8318 (tp30) cc_final: 0.7907 (tp30) REVERT: B 286 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8522 (mtpt) REVERT: B 339 SER cc_start: 0.8316 (m) cc_final: 0.8055 (t) outliers start: 92 outliers final: 44 residues processed: 565 average time/residue: 0.3070 time to fit residues: 274.0320 Evaluate side-chains 480 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 429 time to evaluate : 2.448 ------------------------------------------------------------------------------- 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 370 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 901 GLU 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 1139 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1605 GLN Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1761 SER Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1812 ASP Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2022 SER Chi-restraints excluded: chain A residue 2103 GLN Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2214 LEU Chi-restraints excluded: chain A residue 2234 HIS Chi-restraints excluded: chain A residue 2387 LEU Chi-restraints excluded: chain A residue 2455 THR 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 2697 VAL Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2815 HIS 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 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 131 optimal weight: 0.0370 chunk 73 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 237 optimal weight: 0.0020 chunk 256 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 235 optimal weight: 0.0980 chunk 80 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.6270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 378 GLN A1146 ASN A1272 GLN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 HIS A1589 GLN ** A1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN A2048 HIS A2103 GLN ** A2236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2622 ASN A2669 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 357 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20885 Z= 0.200 Angle : 0.663 9.684 28374 Z= 0.322 Chirality : 0.042 0.193 3395 Planarity : 0.005 0.074 3576 Dihedral : 6.306 65.529 2804 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 4.52 % Allowed : 14.05 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.14), residues: 2575 helix: -4.36 (0.08), residues: 1340 sheet: None (None), residues: 0 loop : -1.20 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 345 HIS 0.016 0.001 HIS A2234 PHE 0.020 0.001 PHE A2383 TYR 0.010 0.001 TYR A3013 ARG 0.006 0.000 ARG A2528 *********************** 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 586 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 483 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ASN cc_start: 0.7313 (t0) cc_final: 0.7026 (t0) REVERT: A 243 GLU cc_start: 0.6784 (mp0) cc_final: 0.5905 (mp0) REVERT: A 683 LEU cc_start: 0.8832 (tt) cc_final: 0.8586 (tp) REVERT: A 731 TYR cc_start: 0.8272 (m-80) cc_final: 0.7623 (m-80) REVERT: A 745 TYR cc_start: 0.8856 (m-80) cc_final: 0.8572 (m-80) REVERT: A 994 MET cc_start: 0.8529 (tpp) cc_final: 0.8299 (tpp) REVERT: A 1088 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8527 (tp) REVERT: A 1146 ASN cc_start: 0.8056 (t0) cc_final: 0.7838 (t0) REVERT: A 1355 PHE cc_start: 0.7831 (t80) cc_final: 0.7620 (t80) REVERT: A 1356 MET cc_start: 0.8459 (tpp) cc_final: 0.7820 (tpp) REVERT: A 1485 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8063 (mt-10) REVERT: A 1501 SER cc_start: 0.8523 (p) cc_final: 0.8048 (t) REVERT: A 1640 SER cc_start: 0.9000 (p) cc_final: 0.8666 (t) REVERT: A 1647 MET cc_start: 0.7570 (tpt) cc_final: 0.7283 (tpt) REVERT: A 1670 SER cc_start: 0.9211 (p) cc_final: 0.8899 (t) REVERT: A 1702 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8475 (pt) REVERT: A 1742 GLN cc_start: 0.7434 (tt0) cc_final: 0.6937 (tt0) REVERT: A 1743 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8414 (tm) REVERT: A 1923 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (tm) REVERT: A 2135 GLU cc_start: 0.5757 (tt0) cc_final: 0.5420 (pm20) REVERT: A 2272 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8104 (tm-30) REVERT: A 2510 MET cc_start: 0.7927 (tmt) cc_final: 0.6888 (tmt) REVERT: A 2567 HIS cc_start: 0.7337 (p-80) cc_final: 0.7023 (p-80) REVERT: A 2570 TYR cc_start: 0.5434 (m-80) cc_final: 0.4136 (m-80) REVERT: A 2695 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 2712 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: A 2713 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7824 (t80) REVERT: A 2730 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7356 (tt0) REVERT: A 2918 MET cc_start: 0.6675 (mmt) cc_final: 0.6172 (mmt) REVERT: B 92 GLU cc_start: 0.8435 (tp30) cc_final: 0.8007 (tp30) REVERT: B 197 TYR cc_start: 0.7967 (m-80) cc_final: 0.7595 (m-80) outliers start: 103 outliers final: 58 residues processed: 543 average time/residue: 0.3097 time to fit residues: 263.6486 Evaluate side-chains 487 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 423 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 370 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 901 GLU 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 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1088 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 1290 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1425 VAL Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1753 THR 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 1820 SER Chi-restraints excluded: chain A residue 1916 ILE Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1924 ILE Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2210 LEU 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 2387 LEU Chi-restraints excluded: chain A residue 2470 VAL 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 2579 LEU 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 2712 GLN 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 216 SER 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 234 optimal weight: 0.0980 chunk 178 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 238 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1310 GLN A1533 HIS ** A1595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1852 GLN ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2669 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3017 GLN ** B 119 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20885 Z= 0.149 Angle : 0.618 10.704 28374 Z= 0.297 Chirality : 0.040 0.206 3395 Planarity : 0.004 0.069 3576 Dihedral : 5.619 61.218 2802 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 3.86 % Allowed : 16.12 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.15), residues: 2575 helix: -3.90 (0.09), residues: 1340 sheet: None (None), residues: 0 loop : -0.96 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2573 HIS 0.007 0.001 HIS A2665 PHE 0.018 0.001 PHE A2383 TYR 0.019 0.001 TYR A2737 ARG 0.004 0.000 ARG A2528 *********************** 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 559 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 471 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ASP cc_start: 0.6646 (m-30) cc_final: 0.6246 (m-30) REVERT: A 683 LEU cc_start: 0.8842 (tt) cc_final: 0.8603 (tp) REVERT: A 731 TYR cc_start: 0.8272 (m-80) cc_final: 0.7492 (m-80) REVERT: A 745 TYR cc_start: 0.8718 (m-80) cc_final: 0.8278 (m-80) REVERT: A 1088 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 1271 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.7857 (m) REVERT: A 1424 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 1484 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.7247 (ttp-110) REVERT: A 1501 SER cc_start: 0.8509 (p) cc_final: 0.7998 (t) REVERT: A 1640 SER cc_start: 0.8971 (p) cc_final: 0.8648 (t) REVERT: A 1743 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8279 (tm) REVERT: A 1905 ASN cc_start: 0.8959 (p0) cc_final: 0.8403 (p0) REVERT: A 1923 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7810 (tm) REVERT: A 2510 MET cc_start: 0.7818 (tmt) cc_final: 0.6875 (tmt) REVERT: A 2668 SER cc_start: 0.8477 (m) cc_final: 0.8193 (t) REVERT: A 2713 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7731 (t80) REVERT: A 2730 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7295 (tt0) REVERT: A 2736 GLN cc_start: 0.6829 (pp30) cc_final: 0.6397 (pp30) REVERT: A 2737 TYR cc_start: 0.7840 (m-80) cc_final: 0.7402 (m-80) REVERT: B 92 GLU cc_start: 0.8518 (tp30) cc_final: 0.8066 (tp30) outliers start: 88 outliers final: 49 residues processed: 515 average time/residue: 0.3157 time to fit residues: 254.8731 Evaluate side-chains 470 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 415 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 710 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 901 GLU 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 1074 TRP Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1290 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1513 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1812 ASP Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1923 LEU 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 2137 ASN Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2470 VAL Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL 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 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 2998 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 295 LEU 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 210 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 362 GLN A 844 GLN A 900 GLN A1150 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN A1708 ASN ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS A2236 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2299 HIS A2305 HIS A2459 GLN A2526 GLN A2552 GLN ** A2563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 20885 Z= 0.477 Angle : 0.831 12.678 28374 Z= 0.406 Chirality : 0.049 0.215 3395 Planarity : 0.006 0.077 3576 Dihedral : 6.432 66.931 2800 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.79 % Rotamer: Outliers : 5.05 % Allowed : 17.13 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.15), residues: 2575 helix: -3.57 (0.10), residues: 1517 sheet: None (None), residues: 0 loop : -1.31 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1041 HIS 0.009 0.002 HIS A2259 PHE 0.029 0.003 PHE A2205 TYR 0.021 0.002 TYR A2737 ARG 0.010 0.001 ARG A1941 *********************** 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 578 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 463 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.7686 (m-40) cc_final: 0.7453 (t0) REVERT: A 202 LEU cc_start: 0.8282 (tt) cc_final: 0.7878 (tp) REVERT: A 663 LYS cc_start: 0.5738 (tptp) cc_final: 0.5515 (tptt) REVERT: A 683 LEU cc_start: 0.9027 (tt) cc_final: 0.8794 (tp) REVERT: A 731 TYR cc_start: 0.8461 (m-80) cc_final: 0.7761 (m-80) REVERT: A 745 TYR cc_start: 0.8954 (m-80) cc_final: 0.8447 (m-80) REVERT: A 771 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9136 (tp) REVERT: A 808 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8446 (mtp85) REVERT: A 953 GLN cc_start: 0.8256 (tt0) cc_final: 0.7996 (mt0) REVERT: A 1102 ARG cc_start: 0.4748 (mmt180) cc_final: 0.4461 (mpt180) REVERT: A 1355 PHE cc_start: 0.7604 (t80) cc_final: 0.6964 (t80) REVERT: A 1424 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 1501 SER cc_start: 0.8956 (p) cc_final: 0.8661 (t) REVERT: A 1640 SER cc_start: 0.8984 (p) cc_final: 0.8719 (t) REVERT: A 1652 MET cc_start: 0.8113 (tmm) cc_final: 0.7732 (ttt) REVERT: A 1734 GLU cc_start: 0.7745 (tp30) cc_final: 0.7417 (mm-30) REVERT: A 1742 GLN cc_start: 0.7878 (tt0) cc_final: 0.7089 (tt0) REVERT: A 1743 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8542 (tm) REVERT: A 1886 ASN cc_start: 0.8425 (t0) cc_final: 0.7987 (m-40) REVERT: A 1923 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8289 (tm) REVERT: A 2135 GLU cc_start: 0.6015 (tt0) cc_final: 0.5709 (pm20) REVERT: A 2424 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7777 (t80) REVERT: A 2510 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7761 (tmt) REVERT: A 2564 ILE cc_start: 0.9311 (mm) cc_final: 0.9090 (tt) REVERT: A 2674 LEU cc_start: 0.8839 (mt) cc_final: 0.8483 (tt) REVERT: A 2713 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 2730 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7465 (tt0) REVERT: A 2839 TYR cc_start: 0.7076 (m-80) cc_final: 0.6845 (m-80) REVERT: A 2952 GLU cc_start: 0.7493 (tt0) cc_final: 0.7011 (mp0) REVERT: A 3013 TYR cc_start: 0.8591 (t80) cc_final: 0.8324 (t80) REVERT: B 92 GLU cc_start: 0.8563 (tp30) cc_final: 0.8294 (tp30) REVERT: B 324 SER cc_start: 0.9175 (p) cc_final: 0.8955 (t) outliers start: 115 outliers final: 80 residues processed: 536 average time/residue: 0.3098 time to fit residues: 262.3196 Evaluate side-chains 503 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 416 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL 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 1242 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1270 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 1424 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 1511 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1670 SER 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 1772 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain A residue 1906 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1923 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 2012 VAL Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2137 ASN 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 2358 MET Chi-restraints excluded: chain A residue 2424 PHE 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 2514 VAL Chi-restraints excluded: chain A residue 2562 GLU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2598 ASN Chi-restraints excluded: chain A residue 2607 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 2779 LEU Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2815 HIS Chi-restraints excluded: chain A residue 2955 SER Chi-restraints excluded: chain A residue 2956 VAL 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 178 LEU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 209 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 399 GLN ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1781 HIS ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2669 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3041 GLN A3081 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20885 Z= 0.193 Angle : 0.646 11.794 28374 Z= 0.311 Chirality : 0.041 0.224 3395 Planarity : 0.004 0.070 3576 Dihedral : 5.812 64.688 2800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 3.91 % Allowed : 19.85 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.15), residues: 2575 helix: -3.12 (0.11), residues: 1518 sheet: None (None), residues: 0 loop : -1.07 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 345 HIS 0.011 0.001 HIS A2567 PHE 0.027 0.001 PHE A2205 TYR 0.015 0.001 TYR A2737 ARG 0.006 0.000 ARG A2219 *********************** 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 529 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 440 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.7514 (m-40) cc_final: 0.7287 (t0) REVERT: A 141 MET cc_start: 0.6873 (mmp) cc_final: 0.6577 (ptt) REVERT: A 683 LEU cc_start: 0.8990 (tt) cc_final: 0.8714 (tp) REVERT: A 731 TYR cc_start: 0.8317 (m-80) cc_final: 0.7651 (m-80) REVERT: A 745 TYR cc_start: 0.8811 (m-80) cc_final: 0.8469 (m-80) REVERT: A 930 LEU cc_start: 0.9117 (mt) cc_final: 0.8733 (mt) REVERT: A 1088 LEU cc_start: 0.8808 (tm) cc_final: 0.8464 (tp) REVERT: A 1102 ARG cc_start: 0.4372 (mmt180) cc_final: 0.4111 (mpt180) REVERT: A 1271 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 1355 PHE cc_start: 0.7699 (t80) cc_final: 0.7059 (t80) REVERT: A 1501 SER cc_start: 0.8828 (p) cc_final: 0.8490 (t) REVERT: A 1584 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: A 1640 SER cc_start: 0.9012 (p) cc_final: 0.8782 (t) REVERT: A 1734 GLU cc_start: 0.7635 (tp30) cc_final: 0.7400 (mm-30) REVERT: A 1743 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8442 (tm) REVERT: A 1886 ASN cc_start: 0.8129 (t0) cc_final: 0.7875 (t0) REVERT: A 1921 GLN cc_start: 0.7322 (mt0) cc_final: 0.7028 (mt0) REVERT: A 1923 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8001 (tm) REVERT: A 2010 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6710 (mtp180) REVERT: A 2014 MET cc_start: 0.6392 (mtp) cc_final: 0.6074 (mtm) REVERT: A 2024 MET cc_start: 0.7367 (mmm) cc_final: 0.6472 (mmm) REVERT: A 2510 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7559 (tmt) REVERT: A 2570 TYR cc_start: 0.4302 (m-80) cc_final: 0.3945 (m-80) REVERT: A 2674 LEU cc_start: 0.8843 (mt) cc_final: 0.8447 (tt) REVERT: A 2713 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8300 (t80) REVERT: A 2730 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7500 (tt0) REVERT: A 2736 GLN cc_start: 0.7405 (pp30) cc_final: 0.7110 (pp30) REVERT: A 2839 TYR cc_start: 0.7388 (m-80) cc_final: 0.7166 (m-10) REVERT: A 2854 MET cc_start: 0.8126 (mmt) cc_final: 0.7562 (mmt) REVERT: A 2912 MET cc_start: 0.8972 (mmt) cc_final: 0.8683 (tpt) REVERT: A 2918 MET cc_start: 0.6846 (mmt) cc_final: 0.6590 (tpp) REVERT: A 3047 MET cc_start: 0.6860 (tpt) cc_final: 0.6632 (tpt) REVERT: A 3081 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: B 92 GLU cc_start: 0.8557 (tp30) cc_final: 0.8233 (tp30) outliers start: 89 outliers final: 55 residues processed: 494 average time/residue: 0.3014 time to fit residues: 235.4329 Evaluate side-chains 469 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 407 time to evaluate : 2.354 ------------------------------------------------------------------------------- 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 237 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 979 ILE 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 1225 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1906 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2137 ASN Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2510 MET Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2543 LEU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2598 ASN 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 2786 LEU Chi-restraints excluded: chain A residue 2998 LEU Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3081 GLN Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 295 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 243 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1091 ASN ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN ** A1765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2590 HIS A2669 GLN A2824 HIS ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3085 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20885 Z= 0.388 Angle : 0.773 12.210 28374 Z= 0.373 Chirality : 0.047 0.242 3395 Planarity : 0.005 0.074 3576 Dihedral : 6.186 65.673 2800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 5.01 % Allowed : 19.98 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.15), residues: 2575 helix: -2.89 (0.11), residues: 1593 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 345 HIS 0.009 0.001 HIS A2567 PHE 0.027 0.002 PHE A 798 TYR 0.019 0.002 TYR A2211 ARG 0.009 0.001 ARG A2962 *********************** 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 553 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 439 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.6362 (t0) cc_final: 0.6155 (t0) REVERT: A 105 ASN cc_start: 0.7866 (m-40) cc_final: 0.7613 (t0) REVERT: A 700 ASP cc_start: 0.8479 (t70) cc_final: 0.8276 (t0) REVERT: A 731 TYR cc_start: 0.8450 (m-80) cc_final: 0.7774 (m-80) REVERT: A 745 TYR cc_start: 0.8923 (m-80) cc_final: 0.8480 (m-80) REVERT: A 930 LEU cc_start: 0.9190 (mt) cc_final: 0.8777 (mt) REVERT: A 1355 PHE cc_start: 0.7735 (t80) cc_final: 0.7112 (t80) REVERT: A 1475 PHE cc_start: 0.8375 (m-80) cc_final: 0.8140 (m-80) REVERT: A 1501 SER cc_start: 0.8878 (p) cc_final: 0.8585 (t) REVERT: A 1652 MET cc_start: 0.8143 (tmm) cc_final: 0.7680 (ttt) REVERT: A 1733 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 1734 GLU cc_start: 0.7794 (tp30) cc_final: 0.7436 (mm-30) REVERT: A 1742 GLN cc_start: 0.7808 (tt0) cc_final: 0.7119 (tt0) REVERT: A 1743 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8637 (tm) REVERT: A 1895 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 1921 GLN cc_start: 0.7296 (mt0) cc_final: 0.6971 (mt0) REVERT: A 1923 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8274 (tm) REVERT: A 1929 GLU cc_start: 0.8367 (tp30) cc_final: 0.8120 (mt-10) REVERT: A 1948 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 2014 MET cc_start: 0.7140 (mtp) cc_final: 0.6764 (mtm) REVERT: A 2024 MET cc_start: 0.7285 (mmm) cc_final: 0.6659 (mmm) REVERT: A 2397 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7847 (mtp85) REVERT: A 2674 LEU cc_start: 0.8937 (mt) cc_final: 0.8552 (tt) REVERT: A 2713 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8511 (t80) REVERT: A 2730 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7543 (tt0) REVERT: A 2737 TYR cc_start: 0.8373 (m-80) cc_final: 0.6973 (m-80) REVERT: A 2854 MET cc_start: 0.8087 (mmt) cc_final: 0.7486 (mmt) REVERT: A 2918 MET cc_start: 0.6539 (mmt) cc_final: 0.6228 (tpp) REVERT: B 92 GLU cc_start: 0.8564 (tp30) cc_final: 0.8284 (tp30) outliers start: 114 outliers final: 83 residues processed: 511 average time/residue: 0.3096 time to fit residues: 251.3197 Evaluate side-chains 488 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 400 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 237 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 313 THR 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 698 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 979 ILE 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 1242 THR 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 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 1490 ILE Chi-restraints excluded: chain A residue 1498 VAL Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1646 ASP Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1820 SER Chi-restraints excluded: chain A residue 1895 LEU Chi-restraints excluded: chain A residue 1906 LEU Chi-restraints excluded: chain A residue 1912 LEU Chi-restraints excluded: chain A residue 1923 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 2012 VAL Chi-restraints excluded: chain A residue 2022 SER Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2137 ASN 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 2253 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2369 VAL Chi-restraints excluded: chain A residue 2494 ILE Chi-restraints excluded: chain A residue 2496 VAL Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2543 LEU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2598 ASN Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2705 ASP Chi-restraints excluded: chain A residue 2713 PHE Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2815 HIS 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 131 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 HIS A1657 ASN ** A1765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS A2259 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2563 ASN A2669 GLN A2822 GLN A2872 HIS ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3041 GLN A3085 ASN B 106 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20885 Z= 0.193 Angle : 0.658 13.653 28374 Z= 0.313 Chirality : 0.041 0.237 3395 Planarity : 0.004 0.069 3576 Dihedral : 5.669 63.845 2800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 3.95 % Allowed : 21.39 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2575 helix: -2.54 (0.12), residues: 1557 sheet: None (None), residues: 0 loop : -1.01 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A2573 HIS 0.011 0.001 HIS A2567 PHE 0.030 0.001 PHE A2205 TYR 0.027 0.001 TYR A2211 ARG 0.006 0.000 ARG A2962 *********************** 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 509 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 419 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASP cc_start: 0.6276 (t0) cc_final: 0.6060 (t0) REVERT: A 105 ASN cc_start: 0.7678 (m-40) cc_final: 0.7450 (t0) REVERT: A 731 TYR cc_start: 0.8329 (m-80) cc_final: 0.7603 (m-80) REVERT: A 745 TYR cc_start: 0.8811 (m-80) cc_final: 0.8467 (m-80) REVERT: A 820 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8485 (tmmt) REVERT: A 930 LEU cc_start: 0.9144 (mt) cc_final: 0.8823 (mt) REVERT: A 989 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7740 (pt) REVERT: A 1088 LEU cc_start: 0.8835 (tm) cc_final: 0.8461 (tp) REVERT: A 1271 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 1284 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8396 (mmtp) REVERT: A 1355 PHE cc_start: 0.7713 (t80) cc_final: 0.7073 (t80) REVERT: A 1501 SER cc_start: 0.8786 (p) cc_final: 0.8496 (t) REVERT: A 1652 MET cc_start: 0.8155 (tmm) cc_final: 0.7763 (ttt) REVERT: A 1734 GLU cc_start: 0.7755 (tp30) cc_final: 0.7332 (mm-30) REVERT: A 1743 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8522 (tm) REVERT: A 1923 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8018 (tm) REVERT: A 1948 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 2010 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6901 (mtp180) REVERT: A 2014 MET cc_start: 0.7079 (mtp) cc_final: 0.6614 (mtm) REVERT: A 2024 MET cc_start: 0.7216 (mmm) cc_final: 0.6686 (mmm) REVERT: A 2454 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7963 (p-90) REVERT: A 2510 MET cc_start: 0.8476 (tmm) cc_final: 0.7674 (tmm) REVERT: A 2522 CYS cc_start: 0.8465 (t) cc_final: 0.8197 (t) REVERT: A 2674 LEU cc_start: 0.8918 (mt) cc_final: 0.8532 (tt) REVERT: A 2708 THR cc_start: 0.8681 (p) cc_final: 0.8378 (t) REVERT: A 2730 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7511 (tt0) REVERT: A 2736 GLN cc_start: 0.7347 (pp30) cc_final: 0.6878 (pp30) REVERT: A 2839 TYR cc_start: 0.7499 (m-10) cc_final: 0.7257 (m-10) REVERT: A 2854 MET cc_start: 0.8041 (mmt) cc_final: 0.7806 (mmt) REVERT: A 2918 MET cc_start: 0.6876 (mmt) cc_final: 0.6599 (tpp) REVERT: B 92 GLU cc_start: 0.8670 (tp30) cc_final: 0.8327 (tp30) outliers start: 90 outliers final: 59 residues processed: 476 average time/residue: 0.3067 time to fit residues: 231.5022 Evaluate side-chains 472 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 407 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1011 THR 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 1242 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1285 CYS Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1438 VAL 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 1621 ILE Chi-restraints excluded: chain A residue 1651 SER Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1785 SER Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1906 LEU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2137 ASN Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2253 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 2496 VAL Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2543 LEU Chi-restraints excluded: chain A residue 2573 TRP Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2598 ASN Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2705 ASP Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 178 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 228 optimal weight: 1.9990 chunk 241 optimal weight: 0.0370 chunk 219 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 240 optimal weight: 0.0470 chunk 141 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 71 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 302 HIS A 362 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN A1765 HIS ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2552 GLN A2563 ASN A2568 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20885 Z= 0.158 Angle : 0.637 14.308 28374 Z= 0.302 Chirality : 0.040 0.274 3395 Planarity : 0.004 0.066 3576 Dihedral : 5.085 58.933 2798 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 2.77 % Allowed : 22.75 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.16), residues: 2575 helix: -2.08 (0.12), residues: 1517 sheet: None (None), residues: 0 loop : -0.91 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A2573 HIS 0.010 0.001 HIS A2567 PHE 0.028 0.001 PHE A2205 TYR 0.028 0.001 TYR A2211 ARG 0.013 0.000 ARG A3075 *********************** 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 491 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 428 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.7633 (m110) cc_final: 0.7386 (t0) REVERT: A 744 GLN cc_start: 0.8483 (pm20) cc_final: 0.7550 (pt0) REVERT: A 745 TYR cc_start: 0.8727 (m-80) cc_final: 0.8340 (m-80) REVERT: A 820 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8492 (tmmt) REVERT: A 930 LEU cc_start: 0.9102 (mt) cc_final: 0.8835 (mt) REVERT: A 989 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7632 (pt) REVERT: A 1088 LEU cc_start: 0.8524 (tm) cc_final: 0.8036 (tp) REVERT: A 1271 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.7935 (m) REVERT: A 1284 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8308 (mmtp) REVERT: A 1501 SER cc_start: 0.8732 (p) cc_final: 0.8410 (t) REVERT: A 1652 MET cc_start: 0.8061 (tmm) cc_final: 0.7716 (ttt) REVERT: A 1743 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8449 (tm) REVERT: A 1921 GLN cc_start: 0.7723 (mt0) cc_final: 0.7074 (mt0) REVERT: A 1923 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (tt) REVERT: A 1948 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 2010 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6763 (mtp180) REVERT: A 2014 MET cc_start: 0.7245 (mtp) cc_final: 0.6781 (mtm) REVERT: A 2510 MET cc_start: 0.8418 (tmm) cc_final: 0.7595 (tmm) REVERT: A 2522 CYS cc_start: 0.8500 (t) cc_final: 0.8009 (t) REVERT: A 2674 LEU cc_start: 0.8862 (mt) cc_final: 0.8487 (tt) REVERT: A 2708 THR cc_start: 0.8721 (p) cc_final: 0.8426 (t) REVERT: A 2730 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7530 (tt0) REVERT: A 2736 GLN cc_start: 0.7299 (pp30) cc_final: 0.6483 (pp30) REVERT: A 2737 TYR cc_start: 0.8173 (m-80) cc_final: 0.6750 (m-80) REVERT: A 2839 TYR cc_start: 0.7470 (m-10) cc_final: 0.7239 (m-10) REVERT: A 3004 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7288 (p90) REVERT: A 3047 MET cc_start: 0.6431 (tpp) cc_final: 0.5810 (tpp) REVERT: B 92 GLU cc_start: 0.8641 (tp30) cc_final: 0.8387 (tp30) REVERT: B 154 ASP cc_start: 0.7488 (m-30) cc_final: 0.7027 (m-30) outliers start: 63 outliers final: 40 residues processed: 467 average time/residue: 0.3394 time to fit residues: 252.5080 Evaluate side-chains 446 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 400 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 710 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 989 ILE 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 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 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 2235 LEU 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 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2543 LEU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 3004 TYR Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 295 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 233 optimal weight: 30.0000 chunk 153 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 117 optimal weight: 0.5980 chunk 172 optimal weight: 0.3980 chunk 260 optimal weight: 0.0470 chunk 239 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 159 optimal weight: 7.9990 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN A1730 ASN ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2048 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2367 GLN ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20885 Z= 0.149 Angle : 0.637 17.211 28374 Z= 0.296 Chirality : 0.039 0.263 3395 Planarity : 0.004 0.065 3576 Dihedral : 4.821 56.306 2798 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 2.06 % Allowed : 23.28 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.17), residues: 2575 helix: -1.69 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.87 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A2454 HIS 0.010 0.001 HIS A2567 PHE 0.027 0.001 PHE A2205 TYR 0.023 0.001 TYR A2211 ARG 0.009 0.000 ARG A1941 ********************** 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 480 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 433 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 184 TRP cc_start: 0.5789 (m-10) cc_final: 0.5547 (m-10) REVERT: A 744 GLN cc_start: 0.8483 (pm20) cc_final: 0.7554 (pt0) REVERT: A 745 TYR cc_start: 0.8656 (m-80) cc_final: 0.8281 (m-80) REVERT: A 820 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8468 (tmmt) REVERT: A 930 LEU cc_start: 0.9040 (mt) cc_final: 0.8784 (mt) REVERT: A 989 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7568 (pt) REVERT: A 991 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7581 (p0) REVERT: A 994 MET cc_start: 0.8637 (tpp) cc_final: 0.7946 (tpp) REVERT: A 1152 LEU cc_start: 0.8988 (mt) cc_final: 0.8711 (mp) REVERT: A 1271 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.7899 (m) REVERT: A 1284 LYS cc_start: 0.8537 (mmmm) cc_final: 0.8325 (mmtp) REVERT: A 1501 SER cc_start: 0.8698 (p) cc_final: 0.8377 (t) REVERT: A 1652 MET cc_start: 0.8042 (tmm) cc_final: 0.7749 (ttt) REVERT: A 1733 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7431 (pt0) REVERT: A 1743 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8440 (tm) REVERT: A 1921 GLN cc_start: 0.7790 (mt0) cc_final: 0.7112 (mt0) REVERT: A 1923 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7849 (tt) REVERT: A 2010 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6716 (mtp180) REVERT: A 2014 MET cc_start: 0.6813 (mtp) cc_final: 0.6354 (mtm) REVERT: A 2522 CYS cc_start: 0.8298 (t) cc_final: 0.7975 (t) REVERT: A 2623 SER cc_start: 0.7425 (m) cc_final: 0.7191 (t) REVERT: A 2668 SER cc_start: 0.8704 (m) cc_final: 0.8473 (t) REVERT: A 2674 LEU cc_start: 0.8854 (mt) cc_final: 0.8487 (tt) REVERT: A 2730 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7471 (tt0) REVERT: A 2736 GLN cc_start: 0.7291 (pp30) cc_final: 0.6572 (pp30) REVERT: A 2737 TYR cc_start: 0.8170 (m-80) cc_final: 0.6743 (m-80) REVERT: A 2854 MET cc_start: 0.7618 (mmt) cc_final: 0.7286 (mmt) REVERT: A 3008 MET cc_start: 0.7178 (tpt) cc_final: 0.6972 (tpt) REVERT: A 3076 MET cc_start: 0.7965 (tmm) cc_final: 0.7576 (tmm) REVERT: B 154 ASP cc_start: 0.7439 (m-30) cc_final: 0.6969 (m-30) REVERT: B 343 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7217 (mt-10) outliers start: 47 outliers final: 37 residues processed: 464 average time/residue: 0.3157 time to fit residues: 230.7994 Evaluate side-chains 441 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 399 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 991 ASP 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 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain A residue 1807 SER Chi-restraints excluded: chain A residue 1842 THR Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1981 SER Chi-restraints excluded: chain A residue 2012 VAL Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2137 ASN Chi-restraints excluded: chain A residue 2169 LEU Chi-restraints excluded: chain A residue 2235 LEU Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2352 ILE Chi-restraints excluded: chain A residue 2512 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2543 LEU Chi-restraints excluded: chain A residue 2579 LEU Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2743 CYS Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 3097 HIS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 220 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 190 optimal weight: 0.0030 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 207 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1083 GLN A1091 ASN ** A1146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1533 HIS ** A1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN A1852 GLN ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 HIS A2048 HIS ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.160339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.137185 restraints weight = 26554.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.137762 restraints weight = 24808.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.138576 restraints weight = 21623.649| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20885 Z= 0.148 Angle : 0.637 15.507 28374 Z= 0.294 Chirality : 0.039 0.257 3395 Planarity : 0.004 0.062 3576 Dihedral : 4.620 54.274 2798 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.11 % Rotamer: Outliers : 2.02 % Allowed : 23.80 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2575 helix: -1.36 (0.13), residues: 1535 sheet: None (None), residues: 0 loop : -0.93 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1041 HIS 0.012 0.001 HIS A2824 PHE 0.026 0.001 PHE A2205 TYR 0.026 0.001 TYR A2211 ARG 0.008 0.000 ARG A2962 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4911.00 seconds wall clock time: 89 minutes 57.41 seconds (5397.41 seconds total)