Starting phenix.real_space_refine on Mon Sep 23 16:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8an1_15529/09_2024/8an1_15529.cif" } resolution = 3.93 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= 0.079 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 189 5.16 5 C 30855 2.51 5 N 8178 2.21 5 O 8568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 47790 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2266 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 15, 'TRANS': 288} Chain breaks: 7 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2259 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 15, 'TRANS': 288} Chain breaks: 7 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 126 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2890 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2825 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 3 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "G" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2843 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 77 Restraints were copied for chains: M, N, K, L, I, J, E, F, O, P, Q, R Time building chain proxies: 17.53, per 1000 atoms: 0.37 Number of scatterers: 47790 At special positions: 0 Unit cell: (225.63, 222.36, 106.82, 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 189 16.00 O 8568 8.00 N 8178 7.00 C 30855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.68 Conformation dependent library (CDL) restraints added in 4.6 seconds 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11838 Finding SS restraints... Secondary structure from input PDB file: 318 helices and 24 sheets defined 69.4% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.816A pdb=" N TYR A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.588A pdb=" N ARG A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 removed outlier: 4.346A pdb=" N ALA A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 145 removed outlier: 4.331A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Proline residue: A 133 - end of helix removed outlier: 3.586A pdb=" N LYS A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 171 through 187 removed outlier: 4.383A pdb=" N GLU A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 4.097A pdb=" N THR A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.659A pdb=" N ALA A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 314 through 327 removed outlier: 3.832A pdb=" N TYR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.513A pdb=" N VAL A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.518A pdb=" N HIS B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.562A pdb=" N LYS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 121 through 145 removed outlier: 4.011A pdb=" N VAL B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ARG B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.503A pdb=" N LYS B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.397A pdb=" N GLU B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.817A pdb=" N ALA B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.680A pdb=" N LEU B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.623A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 4.116A pdb=" N TYR B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 332 through 352 removed outlier: 4.827A pdb=" N ALA B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 44 removed outlier: 4.017A pdb=" N GLN C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.508A pdb=" N ARG C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 removed outlier: 4.069A pdb=" N GLY C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 144 removed outlier: 3.774A pdb=" N ILE C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Proline residue: C 133 - end of helix removed outlier: 3.657A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 171 through 185 removed outlier: 3.514A pdb=" N HIS C 185 " --> pdb=" O CYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.756A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 253 removed outlier: 3.837A pdb=" N TYR C 246 " --> pdb=" O ASN C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 286 removed outlier: 3.609A pdb=" N VAL C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 307 removed outlier: 4.108A pdb=" N TYR C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 293 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 314 through 326 removed outlier: 4.040A pdb=" N TYR C 318 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 332 through 353 removed outlier: 3.519A pdb=" N VAL C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C 340 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 44 removed outlier: 3.534A pdb=" N GLN D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 57 Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 79 through 88 removed outlier: 3.669A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 removed outlier: 4.025A pdb=" N GLY D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 145 removed outlier: 3.884A pdb=" N ILE D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 171 through 185 removed outlier: 3.874A pdb=" N HIS D 185 " --> pdb=" O CYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 4.139A pdb=" N THR D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 removed outlier: 3.705A pdb=" N ALA D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 219 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 242 through 253 removed outlier: 3.963A pdb=" N TYR D 246 " --> pdb=" O ASN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.618A pdb=" N VAL D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE D 285 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 307 Processing helix chain 'D' and resid 314 through 326 removed outlier: 4.309A pdb=" N TYR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 356 removed outlier: 3.687A pdb=" N VAL D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 354 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU D 355 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 44 removed outlier: 3.622A pdb=" N GLN G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 94 through 111 removed outlier: 3.580A pdb=" N ALA G 98 " --> pdb=" O HIS G 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 106 " --> pdb=" O SER G 102 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU G 108 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 4.051A pdb=" N ILE G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 144 Proline residue: G 133 - end of helix removed outlier: 3.741A pdb=" N PHE G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 167 removed outlier: 3.598A pdb=" N LEU G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.678A pdb=" N HIS G 185 " --> pdb=" O CYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 202 Processing helix chain 'G' and resid 206 through 219 removed outlier: 3.940A pdb=" N ALA G 219 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.880A pdb=" N GLY G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 253 removed outlier: 3.900A pdb=" N TYR G 246 " --> pdb=" O ASN G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 287 removed outlier: 3.582A pdb=" N VAL G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 306 Processing helix chain 'G' and resid 314 through 326 removed outlier: 4.214A pdb=" N TYR G 318 " --> pdb=" O ASN G 314 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU G 321 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 332 through 355 removed outlier: 3.670A pdb=" N VAL G 336 " --> pdb=" O LEU G 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA G 343 " --> pdb=" O ILE G 339 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY G 344 " --> pdb=" O ALA G 340 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN G 354 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU G 355 " --> pdb=" O GLU G 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.850A pdb=" N LEU H 11 " --> pdb=" O ARG H 8 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU H 12 " --> pdb=" O PRO H 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 8 through 12' Processing helix chain 'H' and resid 37 through 45 removed outlier: 4.055A pdb=" N GLN H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 79 through 88 removed outlier: 3.597A pdb=" N ARG H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 110 removed outlier: 4.018A pdb=" N GLY H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 144 removed outlier: 3.829A pdb=" N ARG H 122 " --> pdb=" O PRO H 118 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL H 125 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Proline residue: H 133 - end of helix removed outlier: 3.780A pdb=" N LYS H 144 " --> pdb=" O GLN H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 171 through 185 Processing helix chain 'H' and resid 191 through 202 Processing helix chain 'H' and resid 206 through 219 removed outlier: 3.620A pdb=" N VAL H 210 " --> pdb=" O ASP H 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'H' and resid 242 through 254 removed outlier: 3.906A pdb=" N TYR H 246 " --> pdb=" O ASN H 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 254 " --> pdb=" O CYS H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 286 removed outlier: 3.997A pdb=" N VAL H 273 " --> pdb=" O ASP H 269 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE H 274 " --> pdb=" O PRO H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 307 removed outlier: 4.274A pdb=" N ARG H 305 " --> pdb=" O ALA H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 326 removed outlier: 3.832A pdb=" N TYR H 318 " --> pdb=" O ASN H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 331 No H-bonds generated for 'chain 'H' and resid 329 through 331' Processing helix chain 'H' and resid 332 through 354 removed outlier: 4.751A pdb=" N ALA H 343 " --> pdb=" O ILE H 339 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY H 344 " --> pdb=" O ALA H 340 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP H 345 " --> pdb=" O ARG H 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 346 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN H 354 " --> pdb=" O LYS H 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 61 through 74 removed outlier: 3.815A pdb=" N TYR E 74 " --> pdb=" O HIS E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 88 removed outlier: 3.587A pdb=" N ARG E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 removed outlier: 4.346A pdb=" N ALA E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 145 removed outlier: 4.331A pdb=" N VAL E 126 " --> pdb=" O ARG E 122 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) Proline residue: E 133 - end of helix removed outlier: 3.585A pdb=" N LYS E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 171 through 187 removed outlier: 4.383A pdb=" N GLU E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 203 removed outlier: 4.098A pdb=" N THR E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.659A pdb=" N ALA E 219 " --> pdb=" O VAL E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 Processing helix chain 'E' and resid 242 through 253 Processing helix chain 'E' and resid 271 through 286 Processing helix chain 'E' and resid 291 through 306 Processing helix chain 'E' and resid 314 through 327 removed outlier: 3.832A pdb=" N TYR E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 321 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 332 through 354 removed outlier: 3.512A pdb=" N VAL E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE E 337 " --> pdb=" O PHE E 333 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA E 343 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN E 354 " --> pdb=" O LYS E 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 61 through 75 removed outlier: 3.519A pdb=" N HIS I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 87 removed outlier: 3.562A pdb=" N LYS I 87 " --> pdb=" O ARG I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 110 Processing helix chain 'I' and resid 121 through 145 removed outlier: 4.012A pdb=" N VAL I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL I 126 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ARG I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) Proline residue: I 133 - end of helix removed outlier: 3.503A pdb=" N LYS I 144 " --> pdb=" O GLN I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 167 Processing helix chain 'I' and resid 171 through 187 removed outlier: 4.396A pdb=" N GLU I 187 " --> pdb=" O THR I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 202 Processing helix chain 'I' and resid 206 through 219 removed outlier: 3.817A pdb=" N ALA I 219 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 238 removed outlier: 3.680A pdb=" N LEU I 231 " --> pdb=" O ASN I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 253 Processing helix chain 'I' and resid 271 through 286 Processing helix chain 'I' and resid 291 through 306 removed outlier: 3.622A pdb=" N GLU I 304 " --> pdb=" O LYS I 300 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG I 305 " --> pdb=" O ALA I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 327 removed outlier: 4.116A pdb=" N TYR I 318 " --> pdb=" O ASN I 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 321 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 331 No H-bonds generated for 'chain 'I' and resid 329 through 331' Processing helix chain 'I' and resid 332 through 352 removed outlier: 4.827A pdb=" N ALA I 343 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 44 removed outlier: 4.017A pdb=" N GLN K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 79 through 88 removed outlier: 3.508A pdb=" N ARG K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 110 removed outlier: 4.070A pdb=" N GLY K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 144 removed outlier: 3.773A pdb=" N ILE K 132 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Proline residue: K 133 - end of helix removed outlier: 3.657A pdb=" N LYS K 144 " --> pdb=" O GLN K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 167 Processing helix chain 'K' and resid 171 through 185 removed outlier: 3.513A pdb=" N HIS K 185 " --> pdb=" O CYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 202 Processing helix chain 'K' and resid 206 through 219 Processing helix chain 'K' and resid 225 through 238 removed outlier: 3.756A pdb=" N GLY K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 253 removed outlier: 3.836A pdb=" N TYR K 246 " --> pdb=" O ASN K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 286 removed outlier: 3.609A pdb=" N VAL K 273 " --> pdb=" O ASP K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 307 removed outlier: 4.108A pdb=" N TYR K 292 " --> pdb=" O HIS K 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU K 293 " --> pdb=" O ASP K 289 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG K 305 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER K 307 " --> pdb=" O ALA K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 310 No H-bonds generated for 'chain 'K' and resid 308 through 310' Processing helix chain 'K' and resid 314 through 326 removed outlier: 4.040A pdb=" N TYR K 318 " --> pdb=" O ASN K 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 321 " --> pdb=" O PHE K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 329 through 331 No H-bonds generated for 'chain 'K' and resid 329 through 331' Processing helix chain 'K' and resid 332 through 353 removed outlier: 3.519A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA K 340 " --> pdb=" O VAL K 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 44 removed outlier: 3.534A pdb=" N GLN M 44 " --> pdb=" O GLN M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 57 Processing helix chain 'M' and resid 61 through 76 Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.669A pdb=" N ARG M 83 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS M 88 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 110 removed outlier: 4.025A pdb=" N GLY M 107 " --> pdb=" O ALA M 103 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU M 108 " --> pdb=" O ALA M 104 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 145 removed outlier: 3.885A pdb=" N ILE M 132 " --> pdb=" O LEU M 128 " (cutoff:3.500A) Proline residue: M 133 - end of helix Processing helix chain 'M' and resid 156 through 167 Processing helix chain 'M' and resid 171 through 185 removed outlier: 3.875A pdb=" N HIS M 185 " --> pdb=" O CYS M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 203 removed outlier: 4.138A pdb=" N THR M 203 " --> pdb=" O VAL M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 219 removed outlier: 3.706A pdb=" N ALA M 212 " --> pdb=" O TYR M 208 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA M 219 " --> pdb=" O VAL M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 237 Processing helix chain 'M' and resid 239 through 241 No H-bonds generated for 'chain 'M' and resid 239 through 241' Processing helix chain 'M' and resid 242 through 253 removed outlier: 3.963A pdb=" N TYR M 246 " --> pdb=" O ASN M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 286 removed outlier: 3.618A pdb=" N VAL M 273 " --> pdb=" O ASP M 269 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP M 284 " --> pdb=" O GLU M 280 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE M 285 " --> pdb=" O GLN M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 307 Processing helix chain 'M' and resid 314 through 326 removed outlier: 4.307A pdb=" N TYR M 318 " --> pdb=" O ASN M 314 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU M 321 " --> pdb=" O PHE M 317 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 356 removed outlier: 3.687A pdb=" N VAL M 336 " --> pdb=" O LEU M 332 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE M 337 " --> pdb=" O PHE M 333 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA M 343 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY M 344 " --> pdb=" O ALA M 340 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN M 354 " --> pdb=" O LYS M 350 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU M 355 " --> pdb=" O GLU M 351 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN M 356 " --> pdb=" O GLN M 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 44 removed outlier: 3.622A pdb=" N GLN O 43 " --> pdb=" O GLU O 39 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 79 through 87 Processing helix chain 'O' and resid 94 through 111 removed outlier: 3.580A pdb=" N ALA O 98 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU O 106 " --> pdb=" O SER O 102 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 121 removed outlier: 4.051A pdb=" N ILE O 121 " --> pdb=" O PRO O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 144 Proline residue: O 133 - end of helix removed outlier: 3.741A pdb=" N PHE O 139 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS O 144 " --> pdb=" O GLN O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 167 removed outlier: 3.598A pdb=" N LEU O 165 " --> pdb=" O PHE O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 185 removed outlier: 3.677A pdb=" N HIS O 185 " --> pdb=" O CYS O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 202 Processing helix chain 'O' and resid 206 through 219 removed outlier: 3.941A pdb=" N ALA O 219 " --> pdb=" O VAL O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 238 removed outlier: 3.879A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 253 removed outlier: 3.900A pdb=" N TYR O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 287 removed outlier: 3.582A pdb=" N VAL O 273 " --> pdb=" O ASP O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 289 through 306 Processing helix chain 'O' and resid 314 through 326 removed outlier: 4.215A pdb=" N TYR O 318 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU O 321 " --> pdb=" O PHE O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 329 through 331 No H-bonds generated for 'chain 'O' and resid 329 through 331' Processing helix chain 'O' and resid 332 through 355 removed outlier: 3.670A pdb=" N VAL O 336 " --> pdb=" O LEU O 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA O 343 " --> pdb=" O ILE O 339 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY O 344 " --> pdb=" O ALA O 340 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN O 354 " --> pdb=" O LYS O 350 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU O 355 " --> pdb=" O GLU O 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.850A pdb=" N LEU Q 11 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Q 12 " --> pdb=" O PRO Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 8 through 12' Processing helix chain 'Q' and resid 37 through 45 removed outlier: 4.055A pdb=" N GLN Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 79 through 88 removed outlier: 3.597A pdb=" N ARG Q 83 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS Q 88 " --> pdb=" O ASP Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 110 removed outlier: 4.018A pdb=" N GLY Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR Q 110 " --> pdb=" O LEU Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 144 removed outlier: 3.827A pdb=" N ARG Q 122 " --> pdb=" O PRO Q 118 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA Q 124 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL Q 125 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE Q 132 " --> pdb=" O LEU Q 128 " (cutoff:3.500A) Proline residue: Q 133 - end of helix removed outlier: 3.780A pdb=" N LYS Q 144 " --> pdb=" O GLN Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 156 through 167 Processing helix chain 'Q' and resid 171 through 185 Processing helix chain 'Q' and resid 191 through 202 Processing helix chain 'Q' and resid 206 through 219 removed outlier: 3.621A pdb=" N VAL Q 210 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA Q 219 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 238 Processing helix chain 'Q' and resid 239 through 241 No H-bonds generated for 'chain 'Q' and resid 239 through 241' Processing helix chain 'Q' and resid 242 through 254 removed outlier: 3.905A pdb=" N TYR Q 246 " --> pdb=" O ASN Q 242 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS Q 254 " --> pdb=" O CYS Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 286 removed outlier: 3.998A pdb=" N VAL Q 273 " --> pdb=" O ASP Q 269 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE Q 274 " --> pdb=" O PRO Q 270 " (cutoff:3.500A) Processing helix chain 'Q' and resid 289 through 307 removed outlier: 4.274A pdb=" N ARG Q 305 " --> pdb=" O ALA Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 314 through 326 removed outlier: 3.832A pdb=" N TYR Q 318 " --> pdb=" O ASN Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 331 No H-bonds generated for 'chain 'Q' and resid 329 through 331' Processing helix chain 'Q' and resid 332 through 354 removed outlier: 4.751A pdb=" N ALA Q 343 " --> pdb=" O ILE Q 339 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY Q 344 " --> pdb=" O ALA Q 340 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP Q 345 " --> pdb=" O ARG Q 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU Q 346 " --> pdb=" O VAL Q 342 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN Q 354 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 61 through 74 removed outlier: 3.816A pdb=" N TYR F 74 " --> pdb=" O HIS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 88 removed outlier: 3.587A pdb=" N ARG F 83 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 removed outlier: 4.346A pdb=" N ALA F 98 " --> pdb=" O HIS F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 145 removed outlier: 4.330A pdb=" N VAL F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Proline residue: F 133 - end of helix removed outlier: 3.585A pdb=" N LYS F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 171 through 187 removed outlier: 4.383A pdb=" N GLU F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 removed outlier: 4.098A pdb=" N THR F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 219 removed outlier: 3.658A pdb=" N ALA F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 Processing helix chain 'F' and resid 242 through 253 Processing helix chain 'F' and resid 271 through 286 Processing helix chain 'F' and resid 291 through 306 Processing helix chain 'F' and resid 314 through 327 removed outlier: 3.832A pdb=" N TYR F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY F 320 " --> pdb=" O ASP F 316 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 321 " --> pdb=" O PHE F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 332 through 354 removed outlier: 3.512A pdb=" N VAL F 336 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 337 " --> pdb=" O PHE F 333 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA F 343 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN F 354 " --> pdb=" O LYS F 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 44 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 61 through 75 removed outlier: 3.518A pdb=" N HIS J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 87 removed outlier: 3.563A pdb=" N LYS J 87 " --> pdb=" O ARG J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 110 Processing helix chain 'J' and resid 121 through 145 removed outlier: 4.012A pdb=" N VAL J 125 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL J 126 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ARG J 127 " --> pdb=" O ALA J 123 " (cutoff:3.500A) Proline residue: J 133 - end of helix removed outlier: 3.502A pdb=" N LYS J 144 " --> pdb=" O GLN J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 167 Processing helix chain 'J' and resid 171 through 187 removed outlier: 4.396A pdb=" N GLU J 187 " --> pdb=" O THR J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 Processing helix chain 'J' and resid 206 through 219 removed outlier: 3.817A pdb=" N ALA J 219 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 238 removed outlier: 3.680A pdb=" N LEU J 231 " --> pdb=" O ASN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 253 Processing helix chain 'J' and resid 271 through 286 Processing helix chain 'J' and resid 291 through 306 removed outlier: 3.623A pdb=" N GLU J 304 " --> pdb=" O LYS J 300 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG J 305 " --> pdb=" O ALA J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 removed outlier: 4.116A pdb=" N TYR J 318 " --> pdb=" O ASN J 314 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU J 321 " --> pdb=" O PHE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 331 No H-bonds generated for 'chain 'J' and resid 329 through 331' Processing helix chain 'J' and resid 332 through 352 removed outlier: 4.827A pdb=" N ALA J 343 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY J 344 " --> pdb=" O ALA J 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 44 removed outlier: 4.018A pdb=" N GLN L 44 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 57 Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 79 through 88 removed outlier: 3.508A pdb=" N ARG L 83 " --> pdb=" O LYS L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 110 removed outlier: 4.069A pdb=" N GLY L 107 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 144 removed outlier: 3.773A pdb=" N ILE L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) Proline residue: L 133 - end of helix removed outlier: 3.658A pdb=" N LYS L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 171 through 185 removed outlier: 3.515A pdb=" N HIS L 185 " --> pdb=" O CYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 Processing helix chain 'L' and resid 206 through 219 Processing helix chain 'L' and resid 225 through 238 removed outlier: 3.756A pdb=" N GLY L 238 " --> pdb=" O LEU L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 253 removed outlier: 3.836A pdb=" N TYR L 246 " --> pdb=" O ASN L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 286 removed outlier: 3.610A pdb=" N VAL L 273 " --> pdb=" O ASP L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 307 removed outlier: 4.108A pdb=" N TYR L 292 " --> pdb=" O HIS L 288 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU L 293 " --> pdb=" O ASP L 289 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG L 305 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER L 307 " --> pdb=" O ALA L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 310 No H-bonds generated for 'chain 'L' and resid 308 through 310' Processing helix chain 'L' and resid 314 through 326 removed outlier: 4.040A pdb=" N TYR L 318 " --> pdb=" O ASN L 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU L 321 " --> pdb=" O PHE L 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 331 No H-bonds generated for 'chain 'L' and resid 329 through 331' Processing helix chain 'L' and resid 332 through 353 removed outlier: 3.520A pdb=" N VAL L 336 " --> pdb=" O LEU L 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA L 340 " --> pdb=" O VAL L 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA L 347 " --> pdb=" O ALA L 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 44 removed outlier: 3.535A pdb=" N GLN N 44 " --> pdb=" O GLN N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 61 through 76 Processing helix chain 'N' and resid 79 through 88 removed outlier: 3.669A pdb=" N ARG N 83 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS N 88 " --> pdb=" O ASP N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 110 removed outlier: 4.024A pdb=" N GLY N 107 " --> pdb=" O ALA N 103 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU N 108 " --> pdb=" O ALA N 104 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 110 " --> pdb=" O LEU N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 145 removed outlier: 3.885A pdb=" N ILE N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) Proline residue: N 133 - end of helix Processing helix chain 'N' and resid 156 through 167 Processing helix chain 'N' and resid 171 through 185 removed outlier: 3.875A pdb=" N HIS N 185 " --> pdb=" O CYS N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 203 removed outlier: 4.138A pdb=" N THR N 203 " --> pdb=" O VAL N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 219 removed outlier: 3.705A pdb=" N ALA N 212 " --> pdb=" O TYR N 208 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA N 219 " --> pdb=" O VAL N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 237 Processing helix chain 'N' and resid 239 through 241 No H-bonds generated for 'chain 'N' and resid 239 through 241' Processing helix chain 'N' and resid 242 through 253 removed outlier: 3.963A pdb=" N TYR N 246 " --> pdb=" O ASN N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 286 removed outlier: 3.618A pdb=" N VAL N 273 " --> pdb=" O ASP N 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP N 284 " --> pdb=" O GLU N 280 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE N 285 " --> pdb=" O GLN N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 307 Processing helix chain 'N' and resid 314 through 326 removed outlier: 4.308A pdb=" N TYR N 318 " --> pdb=" O ASN N 314 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU N 321 " --> pdb=" O PHE N 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 356 removed outlier: 3.686A pdb=" N VAL N 336 " --> pdb=" O LEU N 332 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE N 337 " --> pdb=" O PHE N 333 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA N 343 " --> pdb=" O ILE N 339 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN N 354 " --> pdb=" O LYS N 350 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU N 355 " --> pdb=" O GLU N 351 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN N 356 " --> pdb=" O GLN N 352 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 44 removed outlier: 3.622A pdb=" N GLN P 43 " --> pdb=" O GLU P 39 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN P 44 " --> pdb=" O GLN P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 57 Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 79 through 87 Processing helix chain 'P' and resid 94 through 111 removed outlier: 3.579A pdb=" N ALA P 98 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 106 " --> pdb=" O SER P 102 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU P 108 " --> pdb=" O ALA P 104 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 121 removed outlier: 4.050A pdb=" N ILE P 121 " --> pdb=" O PRO P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 144 Proline residue: P 133 - end of helix removed outlier: 3.742A pdb=" N PHE P 139 " --> pdb=" O MET P 135 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS P 144 " --> pdb=" O GLN P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 167 removed outlier: 3.598A pdb=" N LEU P 165 " --> pdb=" O PHE P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 185 removed outlier: 3.677A pdb=" N HIS P 185 " --> pdb=" O CYS P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 Processing helix chain 'P' and resid 206 through 219 removed outlier: 3.941A pdb=" N ALA P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 238 removed outlier: 3.879A pdb=" N GLY P 238 " --> pdb=" O LEU P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 253 removed outlier: 3.900A pdb=" N TYR P 246 " --> pdb=" O ASN P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 287 removed outlier: 3.582A pdb=" N VAL P 273 " --> pdb=" O ASP P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 289 through 306 Processing helix chain 'P' and resid 314 through 326 removed outlier: 4.214A pdb=" N TYR P 318 " --> pdb=" O ASN P 314 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 329 through 331 No H-bonds generated for 'chain 'P' and resid 329 through 331' Processing helix chain 'P' and resid 332 through 355 removed outlier: 3.670A pdb=" N VAL P 336 " --> pdb=" O LEU P 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA P 343 " --> pdb=" O ILE P 339 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY P 344 " --> pdb=" O ALA P 340 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN P 354 " --> pdb=" O LYS P 350 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU P 355 " --> pdb=" O GLU P 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 12 removed outlier: 3.850A pdb=" N LEU R 11 " --> pdb=" O ARG R 8 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU R 12 " --> pdb=" O PRO R 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 8 through 12' Processing helix chain 'R' and resid 37 through 45 removed outlier: 4.055A pdb=" N GLN R 44 " --> pdb=" O GLN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 57 Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'R' and resid 79 through 88 removed outlier: 3.597A pdb=" N ARG R 83 " --> pdb=" O LYS R 79 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS R 88 " --> pdb=" O ASP R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 110 removed outlier: 4.018A pdb=" N GLY R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 144 removed outlier: 3.828A pdb=" N ARG R 122 " --> pdb=" O PRO R 118 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Proline residue: R 133 - end of helix removed outlier: 3.780A pdb=" N LYS R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 167 Processing helix chain 'R' and resid 171 through 185 Processing helix chain 'R' and resid 191 through 202 Processing helix chain 'R' and resid 206 through 219 removed outlier: 3.620A pdb=" N VAL R 210 " --> pdb=" O ASP R 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 238 Processing helix chain 'R' and resid 239 through 241 No H-bonds generated for 'chain 'R' and resid 239 through 241' Processing helix chain 'R' and resid 242 through 254 removed outlier: 3.905A pdb=" N TYR R 246 " --> pdb=" O ASN R 242 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS R 254 " --> pdb=" O CYS R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.999A pdb=" N VAL R 273 " --> pdb=" O ASP R 269 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 307 removed outlier: 4.274A pdb=" N ARG R 305 " --> pdb=" O ALA R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 326 removed outlier: 3.832A pdb=" N TYR R 318 " --> pdb=" O ASN R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 331 No H-bonds generated for 'chain 'R' and resid 329 through 331' Processing helix chain 'R' and resid 332 through 354 removed outlier: 4.752A pdb=" N ALA R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY R 344 " --> pdb=" O ALA R 340 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU R 346 " --> pdb=" O VAL R 342 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN R 354 " --> pdb=" O LYS R 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 25 removed outlier: 4.481A pdb=" N PHE B 23 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 32 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 18 through 19 removed outlier: 5.588A pdb=" N ILE D 364 " --> pdb=" O SER C 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 removed outlier: 3.825A pdb=" N GLU D 32 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 25 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 30 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 12 through 19 removed outlier: 4.651A pdb=" N GLY G 13 " --> pdb=" O ARG H 360 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR H 362 " --> pdb=" O GLY G 13 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE H 364 " --> pdb=" O PRO G 15 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR G 17 " --> pdb=" O ILE H 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 22 through 25 Processing sheet with id=AA8, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'E' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'I' and resid 23 through 25 removed outlier: 4.481A pdb=" N PHE I 23 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU I 32 " --> pdb=" O PHE I 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 18 through 19 removed outlier: 5.589A pdb=" N ILE M 364 " --> pdb=" O SER K 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'M' and resid 22 through 25 removed outlier: 3.825A pdb=" N GLU M 32 " --> pdb=" O PHE M 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP M 25 " --> pdb=" O VAL M 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL M 30 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 12 through 19 removed outlier: 4.650A pdb=" N GLY O 13 " --> pdb=" O ARG Q 360 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR Q 362 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE Q 364 " --> pdb=" O PRO O 15 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR O 17 " --> pdb=" O ILE Q 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 22 through 25 Processing sheet with id=AB7, first strand: chain 'Q' and resid 22 through 24 Processing sheet with id=AB8, first strand: chain 'F' and resid 24 through 25 Processing sheet with id=AB9, first strand: chain 'J' and resid 23 through 25 removed outlier: 4.481A pdb=" N PHE J 23 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU J 32 " --> pdb=" O PHE J 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 19 removed outlier: 5.588A pdb=" N ILE N 364 " --> pdb=" O SER L 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'L' and resid 22 through 25 Processing sheet with id=AC3, first strand: chain 'N' and resid 22 through 25 removed outlier: 3.825A pdb=" N GLU N 32 " --> pdb=" O PHE N 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP N 25 " --> pdb=" O VAL N 30 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL N 30 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 12 through 19 removed outlier: 4.651A pdb=" N GLY P 13 " --> pdb=" O ARG R 360 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR R 362 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE R 364 " --> pdb=" O PRO P 15 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR P 17 " --> pdb=" O ILE R 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'P' and resid 22 through 25 Processing sheet with id=AC6, first strand: chain 'R' and resid 22 through 24 2700 hydrogen bonds defined for protein. 8046 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: 13.53 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9301 1.33 - 1.45: 11890 1.45 - 1.57: 27421 1.57 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 48936 Sorted by residual: bond pdb=" C GLU C 6 " pdb=" O GLU C 6 " ideal model delta sigma weight residual 1.235 1.208 0.026 1.30e-02 5.92e+03 4.11e+00 bond pdb=" N GLU K 6 " pdb=" CA GLU K 6 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.23e-02 6.61e+03 4.01e+00 bond pdb=" N GLU L 6 " pdb=" CA GLU L 6 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.23e-02 6.61e+03 3.91e+00 bond pdb=" C GLU L 6 " pdb=" O GLU L 6 " ideal model delta sigma weight residual 1.235 1.212 0.023 1.30e-02 5.92e+03 3.01e+00 bond pdb=" N GLU C 6 " pdb=" CA GLU C 6 " ideal model delta sigma weight residual 1.454 1.475 -0.021 1.23e-02 6.61e+03 2.91e+00 ... (remaining 48931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 65927 1.68 - 3.36: 585 3.36 - 5.04: 112 5.04 - 6.72: 30 6.72 - 8.40: 15 Bond angle restraints: 66669 Sorted by residual: angle pdb=" OG1 THR R 205 " pdb=" CB THR R 205 " pdb=" CG2 THR R 205 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" OG1 THR Q 205 " pdb=" CB THR Q 205 " pdb=" CG2 THR Q 205 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" OG1 THR H 205 " pdb=" CB THR H 205 " pdb=" CG2 THR H 205 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU N 204 " pdb=" CB LEU N 204 " pdb=" CG LEU N 204 " ideal model delta sigma weight residual 116.30 124.70 -8.40 3.50e+00 8.16e-02 5.75e+00 angle pdb=" CA LEU M 204 " pdb=" CB LEU M 204 " pdb=" CG LEU M 204 " ideal model delta sigma weight residual 116.30 124.69 -8.39 3.50e+00 8.16e-02 5.74e+00 ... (remaining 66664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.19: 26482 13.19 - 26.38: 1652 26.38 - 39.57: 615 39.57 - 52.76: 141 52.76 - 65.96: 69 Dihedral angle restraints: 28959 sinusoidal: 10671 harmonic: 18288 Sorted by residual: dihedral pdb=" CA TYR R 120 " pdb=" C TYR R 120 " pdb=" N ILE R 121 " pdb=" CA ILE R 121 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR Q 120 " pdb=" C TYR Q 120 " pdb=" N ILE Q 121 " pdb=" CA ILE Q 121 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR H 120 " pdb=" C TYR H 120 " pdb=" N ILE H 121 " pdb=" CA ILE H 121 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 28956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5880 0.039 - 0.078: 1364 0.078 - 0.117: 403 0.117 - 0.156: 18 0.156 - 0.195: 9 Chirality restraints: 7674 Sorted by residual: chirality pdb=" CA GLU C 6 " pdb=" N GLU C 6 " pdb=" C GLU C 6 " pdb=" CB GLU C 6 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CA GLU L 6 " pdb=" N GLU L 6 " pdb=" C GLU L 6 " pdb=" CB GLU L 6 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA GLU K 6 " pdb=" N GLU K 6 " pdb=" C GLU K 6 " pdb=" CB GLU K 6 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 7671 not shown) Planarity restraints: 8529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 334 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO J 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 335 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 335 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 334 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 334 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO I 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO I 335 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 335 " 0.020 5.00e-02 4.00e+02 ... (remaining 8526 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1155 2.71 - 3.26: 50493 3.26 - 3.81: 78133 3.81 - 4.35: 86462 4.35 - 4.90: 147749 Nonbonded interactions: 363992 Sorted by model distance: nonbonded pdb=" OE1 GLU M 280 " pdb=" OH TYR M 292 " model vdw 2.168 3.040 nonbonded pdb=" OE1 GLU D 280 " pdb=" OH TYR D 292 " model vdw 2.169 3.040 nonbonded pdb=" OE1 GLU N 280 " pdb=" OH TYR N 292 " model vdw 2.169 3.040 nonbonded pdb=" O ALA R 303 " pdb=" OG SER R 307 " model vdw 2.255 3.040 nonbonded pdb=" O ALA H 303 " pdb=" OG SER H 307 " model vdw 2.255 3.040 ... (remaining 363987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 through 355)) selection = chain 'B' selection = (chain 'E' and (resid 21 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 through 355)) selection = (chain 'F' and (resid 21 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 through 355)) selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 112 or resid 118 through 146 or (resid 147 and (name N or name CA or name C or \ name O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (na \ me N or name CA or name C or name O or name CB )) or resid 155 through 170 or (r \ esid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 t \ hrough 186 or (resid 187 and (name N or name CA or name C or name O or name CB ) \ ) or resid 188 through 221 or (resid 222 and (name N or name CA or name C or nam \ e O or name CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name \ N or name CA or name C or name O or name CB )) or resid 242 through 253 or (resi \ d 254 and (name N or name CA or name C or name O or name CB )) or resid 255 or ( \ resid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 \ through 286 or resid 290 through 292 or (resid 293 and (name N or name CA or nam \ e C or name O or name CB )) or resid 294 through 298 or (resid 299 through 303 a \ nd (name N or name CA or name C or name O or name CB )) or resid 304 through 308 \ or (resid 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 324 or (resid 325 and (name N or name CA or name C or name O or nam \ e CB )) or resid 326 through 354 or (resid 355 and (name N or name CA or name C \ or name O or name CB )) or resid 356 through 377)) selection = (chain 'D' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 146 or (resid 147 and (name N or name CA or name C or name O o \ r name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 221 or (resid 222 and (name N or name CA or name C or name O or na \ me CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name N or name \ CA or name C or name O or name CB )) or resid 242 through 298 or (resid 299 thr \ ough 303 and (name N or name CA or name C or name O or name CB )) or resid 304 t \ hrough 324 or (resid 325 and (name N or name CA or name C or name O or name CB ) \ ) or resid 326 through 377)) selection = (chain 'G' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 112 or resid 118 through \ 152 or (resid 153 through 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 186 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 221 or (resid 222 a \ nd (name N or name CA or name C or name O or name CB )) or resid 223 or resid 22 \ 6 through 240 or (resid 241 and (name N or name CA or name C or name O or name C \ B )) or resid 242 through 286 or resid 290 through 324 or (resid 325 and (name N \ or name CA or name C or name O or name CB )) or resid 326 through 354 or (resid \ 355 and (name N or name CA or name C or name O or name CB )) or resid 356 throu \ gh 377)) selection = (chain 'H' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 253 or (resid 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 or (resid 256 and (name N or name CA or name C or name O or na \ me CB )) or resid 257 through 286 or resid 290 through 292 or (resid 293 and (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 298 or (r \ esid 299 through 303 and (name N or name CA or name C or name O or name CB )) or \ resid 304 through 308 or (resid 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 354 or (resid 355 and (name N or name CA or n \ ame C or name O or name CB )) or resid 356 through 377)) selection = (chain 'K' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 112 or resid 118 through 146 or (resid 147 and (name N or name CA or name C or \ name O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (na \ me N or name CA or name C or name O or name CB )) or resid 155 through 170 or (r \ esid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 t \ hrough 186 or (resid 187 and (name N or name CA or name C or name O or name CB ) \ ) or resid 188 through 221 or (resid 222 and (name N or name CA or name C or nam \ e O or name CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name \ N or name CA or name C or name O or name CB )) or resid 242 through 253 or (resi \ d 254 and (name N or name CA or name C or name O or name CB )) or resid 255 or ( \ resid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 \ through 286 or resid 290 through 292 or (resid 293 and (name N or name CA or nam \ e C or name O or name CB )) or resid 294 through 298 or (resid 299 through 303 a \ nd (name N or name CA or name C or name O or name CB )) or resid 304 through 308 \ or (resid 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 324 or (resid 325 and (name N or name CA or name C or name O or nam \ e CB )) or resid 326 through 354 or (resid 355 and (name N or name CA or name C \ or name O or name CB )) or resid 356 through 377)) selection = (chain 'L' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 112 or resid 118 through 146 or (resid 147 and (name N or name CA or name C or \ name O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (na \ me N or name CA or name C or name O or name CB )) or resid 155 through 170 or (r \ esid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 t \ hrough 186 or (resid 187 and (name N or name CA or name C or name O or name CB ) \ ) or resid 188 through 221 or (resid 222 and (name N or name CA or name C or nam \ e O or name CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name \ N or name CA or name C or name O or name CB )) or resid 242 through 253 or (resi \ d 254 and (name N or name CA or name C or name O or name CB )) or resid 255 or ( \ resid 256 and (name N or name CA or name C or name O or name CB )) or resid 257 \ through 286 or resid 290 through 292 or (resid 293 and (name N or name CA or nam \ e C or name O or name CB )) or resid 294 through 298 or (resid 299 through 303 a \ nd (name N or name CA or name C or name O or name CB )) or resid 304 through 308 \ or (resid 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 324 or (resid 325 and (name N or name CA or name C or name O or nam \ e CB )) or resid 326 through 354 or (resid 355 and (name N or name CA or name C \ or name O or name CB )) or resid 356 through 377)) selection = (chain 'M' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 146 or (resid 147 and (name N or name CA or name C or name O o \ r name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 221 or (resid 222 and (name N or name CA or name C or name O or na \ me CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name N or name \ CA or name C or name O or name CB )) or resid 242 through 298 or (resid 299 thr \ ough 303 and (name N or name CA or name C or name O or name CB )) or resid 304 t \ hrough 324 or (resid 325 and (name N or name CA or name C or name O or name CB ) \ ) or resid 326 through 377)) selection = (chain 'N' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 72 or (resid 73 and (nam \ e N or name CA or name C or name O or name CB )) or resid 74 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 146 or (resid 147 and (name N or name CA or name C or name O o \ r name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 18 \ 6 or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 221 or (resid 222 and (name N or name CA or name C or name O or na \ me CB )) or resid 223 or resid 226 through 240 or (resid 241 and (name N or name \ CA or name C or name O or name CB )) or resid 242 through 298 or (resid 299 thr \ ough 303 and (name N or name CA or name C or name O or name CB )) or resid 304 t \ hrough 324 or (resid 325 and (name N or name CA or name C or name O or name CB ) \ ) or resid 326 through 377)) selection = (chain 'O' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 112 or resid 118 through \ 152 or (resid 153 through 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 186 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 221 or (resid 222 a \ nd (name N or name CA or name C or name O or name CB )) or resid 223 or resid 22 \ 6 through 240 or (resid 241 and (name N or name CA or name C or name O or name C \ B )) or resid 242 through 286 or resid 290 through 324 or (resid 325 and (name N \ or name CA or name C or name O or name CB )) or resid 326 through 354 or (resid \ 355 and (name N or name CA or name C or name O or name CB )) or resid 356 throu \ gh 377)) selection = (chain 'P' and (resid 5 through 62 or (resid 63 through 64 and (name N or name C \ A or name C or name O or name CB )) or resid 65 through 112 or resid 118 through \ 152 or (resid 153 through 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 170 or (resid 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 186 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 221 or (resid 222 a \ nd (name N or name CA or name C or name O or name CB )) or resid 223 or resid 22 \ 6 through 240 or (resid 241 and (name N or name CA or name C or name O or name C \ B )) or resid 242 through 286 or resid 290 through 324 or (resid 325 and (name N \ or name CA or name C or name O or name CB )) or resid 326 through 354 or (resid \ 355 and (name N or name CA or name C or name O or name CB )) or resid 356 throu \ gh 377)) selection = (chain 'Q' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 253 or (resid 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 or (resid 256 and (name N or name CA or name C or name O or na \ me CB )) or resid 257 through 286 or resid 290 through 292 or (resid 293 and (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 298 or (r \ esid 299 through 303 and (name N or name CA or name C or name O or name CB )) or \ resid 304 through 308 or (resid 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 354 or (resid 355 and (name N or name CA or n \ ame C or name O or name CB )) or resid 356 through 377)) selection = (chain 'R' and (resid 5 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 253 or (resid 254 and (name N or name CA or name C or name O or name C \ B )) or resid 255 or (resid 256 and (name N or name CA or name C or name O or na \ me CB )) or resid 257 through 286 or resid 290 through 292 or (resid 293 and (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 298 or (r \ esid 299 through 303 and (name N or name CA or name C or name O or name CB )) or \ resid 304 through 308 or (resid 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 354 or (resid 355 and (name N or name CA or n \ ame C or name O or name CB )) or resid 356 through 377)) } 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=0.00 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.270 Set scattering table: 0.390 Process input model: 73.090 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.002 0.036 48936 Z= 0.118 Angle : 0.468 8.396 66669 Z= 0.235 Chirality : 0.037 0.195 7674 Planarity : 0.004 0.035 8529 Dihedral : 11.040 65.956 17121 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 3.10 % Allowed : 8.89 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.42 (0.11), residues: 6093 helix: 1.88 (0.09), residues: 3837 sheet: None (None), residues: 0 loop : -0.71 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 56 HIS 0.007 0.001 HIS J 249 PHE 0.013 0.001 PHE D 139 TYR 0.008 0.001 TYR H 291 ARG 0.002 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 693 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7606 (tp30) cc_final: 0.7325 (tp30) REVERT: A 317 PHE cc_start: 0.8743 (t80) cc_final: 0.8501 (t80) REVERT: A 321 LEU cc_start: 0.8842 (mm) cc_final: 0.8512 (mm) REVERT: A 348 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.8365 (t-90) REVERT: A 352 GLN cc_start: 0.7818 (mt0) cc_final: 0.6958 (mt0) REVERT: B 126 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 7 PHE cc_start: 0.8635 (t80) cc_final: 0.8316 (t80) REVERT: D 11 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D 147 ASP cc_start: 0.8073 (p0) cc_final: 0.7831 (p0) REVERT: D 276 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8714 (tm-30) REVERT: D 370 ASN cc_start: 0.8739 (m-40) cc_final: 0.8518 (m-40) REVERT: G 91 ASP cc_start: 0.7908 (p0) cc_final: 0.7687 (p0) REVERT: G 281 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8829 (tm-30) REVERT: H 12 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7841 (mm-30) REVERT: H 91 ASP cc_start: 0.7815 (p0) cc_final: 0.7610 (p0) REVERT: E 187 GLU cc_start: 0.7621 (tp30) cc_final: 0.7361 (tp30) REVERT: E 317 PHE cc_start: 0.8679 (t80) cc_final: 0.8423 (t80) REVERT: E 352 GLN cc_start: 0.7994 (mt0) cc_final: 0.7506 (mt0) REVERT: E 354 ASN cc_start: 0.7783 (p0) cc_final: 0.7559 (p0) REVERT: M 11 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8787 (tt) REVERT: M 94 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7671 (t-90) REVERT: M 147 ASP cc_start: 0.8128 (p0) cc_final: 0.7873 (p0) REVERT: O 91 ASP cc_start: 0.7876 (p0) cc_final: 0.7652 (p0) REVERT: O 281 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8928 (tm-30) REVERT: Q 12 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: F 187 GLU cc_start: 0.7630 (tp30) cc_final: 0.7371 (tp30) REVERT: F 198 MET cc_start: 0.8437 (mmp) cc_final: 0.8113 (mmm) REVERT: F 317 PHE cc_start: 0.8636 (t80) cc_final: 0.8349 (t80) REVERT: F 352 GLN cc_start: 0.7840 (mt0) cc_final: 0.7513 (mt0) REVERT: J 92 SER cc_start: 0.8310 (p) cc_final: 0.8079 (p) REVERT: J 160 ASN cc_start: 0.8422 (t0) cc_final: 0.8214 (t0) REVERT: L 215 VAL cc_start: 0.8957 (t) cc_final: 0.8755 (t) REVERT: N 11 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8934 (tt) REVERT: N 94 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7835 (t-90) REVERT: N 147 ASP cc_start: 0.8061 (p0) cc_final: 0.7776 (p0) REVERT: P 275 LEU cc_start: 0.9327 (mt) cc_final: 0.9127 (mt) REVERT: P 281 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8979 (tm-30) REVERT: R 12 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: R 275 LEU cc_start: 0.9216 (tp) cc_final: 0.9004 (tp) outliers start: 148 outliers final: 54 residues processed: 817 average time/residue: 0.4474 time to fit residues: 621.7247 Evaluate side-chains 506 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 442 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 314 ASN Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 341 ARG Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 203 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 524 optimal weight: 3.9990 chunk 470 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 317 optimal weight: 0.8980 chunk 251 optimal weight: 8.9990 chunk 486 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 563 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 160 ASN C 40 GLN C 160 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS K 40 GLN K 160 ASN M 146 ASN M 150 GLN M 314 ASN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN J 185 HIS L 40 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 GLN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 48936 Z= 0.302 Angle : 0.626 12.998 66669 Z= 0.314 Chirality : 0.041 0.162 7674 Planarity : 0.004 0.052 8529 Dihedral : 5.513 59.278 6903 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.43 % Allowed : 12.40 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.07 (0.11), residues: 6093 helix: 1.56 (0.08), residues: 3900 sheet: None (None), residues: 0 loop : -0.84 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 345 HIS 0.008 0.001 HIS J 249 PHE 0.023 0.002 PHE M 68 TYR 0.022 0.001 TYR F 74 ARG 0.004 0.000 ARG M 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 465 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.9256 (tp) cc_final: 0.9032 (tt) REVERT: A 321 LEU cc_start: 0.8928 (mm) cc_final: 0.8587 (mm) REVERT: A 348 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8505 (t-90) REVERT: A 350 LYS cc_start: 0.9259 (tppt) cc_final: 0.8861 (tttt) REVERT: A 352 GLN cc_start: 0.7923 (mt0) cc_final: 0.7717 (mt0) REVERT: B 94 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5435 (t-90) REVERT: B 126 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 246 TYR cc_start: 0.6173 (t80) cc_final: 0.5610 (t80) REVERT: C 281 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 283 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: D 94 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8158 (t-90) REVERT: D 147 ASP cc_start: 0.8057 (p0) cc_final: 0.7804 (p0) REVERT: D 276 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8899 (tm-30) REVERT: H 12 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: E 350 LYS cc_start: 0.9219 (tppt) cc_final: 0.8936 (tmtt) REVERT: I 85 MET cc_start: 0.9280 (ppp) cc_final: 0.9044 (tmm) REVERT: I 92 SER cc_start: 0.8289 (p) cc_final: 0.8028 (p) REVERT: I 94 HIS cc_start: 0.6581 (OUTLIER) cc_final: 0.5605 (t-90) REVERT: I 350 LYS cc_start: 0.8690 (tptp) cc_final: 0.8325 (tptm) REVERT: K 246 TYR cc_start: 0.6155 (t80) cc_final: 0.5537 (t80) REVERT: M 94 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7774 (t-90) REVERT: M 147 ASP cc_start: 0.8161 (p0) cc_final: 0.7858 (p0) REVERT: O 150 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8068 (tm-30) REVERT: Q 12 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: F 348 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8552 (t-90) REVERT: F 350 LYS cc_start: 0.9320 (tppt) cc_final: 0.8977 (tttt) REVERT: F 352 GLN cc_start: 0.7938 (mt0) cc_final: 0.7338 (mt0) REVERT: J 94 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.5489 (t-90) REVERT: J 160 ASN cc_start: 0.8536 (t0) cc_final: 0.8330 (t0) REVERT: J 350 LYS cc_start: 0.8802 (tptp) cc_final: 0.8367 (tptp) REVERT: L 233 MET cc_start: 0.6370 (tmm) cc_final: 0.6091 (tmm) REVERT: L 266 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6780 (mmmt) REVERT: L 281 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8623 (tm-30) REVERT: N 94 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7706 (t-90) REVERT: N 147 ASP cc_start: 0.8160 (p0) cc_final: 0.7879 (p0) REVERT: N 314 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7677 (p0) REVERT: P 275 LEU cc_start: 0.9329 (mt) cc_final: 0.9092 (mt) REVERT: R 12 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: R 86 MET cc_start: 0.8569 (mtm) cc_final: 0.8364 (mtm) REVERT: R 275 LEU cc_start: 0.9215 (tp) cc_final: 0.9004 (tp) outliers start: 211 outliers final: 126 residues processed: 647 average time/residue: 0.4269 time to fit residues: 480.0096 Evaluate side-chains 570 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 429 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 283 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 283 PHE Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 351 GLU Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 315 VAL Chi-restraints excluded: chain O residue 334 THR Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 341 ARG Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 315 VAL Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 313 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 469 optimal weight: 6.9990 chunk 384 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 564 optimal weight: 0.9980 chunk 610 optimal weight: 20.0000 chunk 503 optimal weight: 9.9990 chunk 560 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 453 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN D 150 GLN ** I 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 146 ASN M 150 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN J 27 GLN J 185 HIS ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48936 Z= 0.177 Angle : 0.569 12.621 66669 Z= 0.280 Chirality : 0.039 0.162 7674 Planarity : 0.004 0.042 8529 Dihedral : 5.277 59.510 6882 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 3.52 % Allowed : 14.37 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.12 (0.11), residues: 6093 helix: 1.60 (0.08), residues: 3900 sheet: None (None), residues: 0 loop : -0.83 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 349 HIS 0.009 0.001 HIS J 185 PHE 0.016 0.001 PHE H 139 TYR 0.019 0.001 TYR F 157 ARG 0.004 0.000 ARG O 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 479 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7882 (tp30) cc_final: 0.7410 (tp30) REVERT: A 321 LEU cc_start: 0.8956 (mm) cc_final: 0.8600 (mm) REVERT: A 348 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.8466 (t-90) REVERT: B 94 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5584 (t-90) REVERT: B 126 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 135 MET cc_start: 0.8231 (mtm) cc_final: 0.7994 (mtm) REVERT: C 246 TYR cc_start: 0.6270 (t80) cc_final: 0.5667 (t80) REVERT: D 11 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8975 (tt) REVERT: D 27 GLN cc_start: 0.7869 (pm20) cc_final: 0.7546 (pp30) REVERT: D 94 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (t-90) REVERT: D 147 ASP cc_start: 0.8040 (p0) cc_final: 0.7827 (p0) REVERT: H 12 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: E 187 GLU cc_start: 0.7662 (tp30) cc_final: 0.7358 (tp30) REVERT: E 350 LYS cc_start: 0.9199 (tppt) cc_final: 0.8967 (tmtt) REVERT: E 352 GLN cc_start: 0.7910 (mt0) cc_final: 0.7599 (mt0) REVERT: I 85 MET cc_start: 0.9355 (ppp) cc_final: 0.9103 (tmm) REVERT: I 92 SER cc_start: 0.8324 (p) cc_final: 0.8069 (p) REVERT: I 94 HIS cc_start: 0.6464 (OUTLIER) cc_final: 0.5610 (t-90) REVERT: I 325 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8680 (tptt) REVERT: I 350 LYS cc_start: 0.8666 (tptp) cc_final: 0.8324 (tptm) REVERT: M 11 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8948 (tt) REVERT: M 94 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7739 (t-90) REVERT: M 147 ASP cc_start: 0.8079 (p0) cc_final: 0.7819 (p0) REVERT: Q 12 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: Q 321 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8638 (mm) REVERT: F 187 GLU cc_start: 0.7942 (tp30) cc_final: 0.7475 (tp30) REVERT: F 350 LYS cc_start: 0.9305 (tppt) cc_final: 0.8967 (tttt) REVERT: J 94 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.5505 (t-90) REVERT: J 100 GLN cc_start: 0.9060 (tt0) cc_final: 0.8724 (tp40) REVERT: J 160 ASN cc_start: 0.8498 (t0) cc_final: 0.8287 (t0) REVERT: J 350 LYS cc_start: 0.8774 (tptp) cc_final: 0.8369 (tptp) REVERT: L 198 MET cc_start: 0.8557 (tpp) cc_final: 0.8345 (tpp) REVERT: N 11 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8975 (tt) REVERT: N 27 GLN cc_start: 0.7921 (pm20) cc_final: 0.7481 (pp30) REVERT: N 94 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7791 (t-90) REVERT: N 147 ASP cc_start: 0.8069 (p0) cc_final: 0.7808 (p0) REVERT: N 242 ASN cc_start: 0.7864 (t0) cc_final: 0.7645 (t0) REVERT: N 314 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7640 (p0) REVERT: P 204 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8821 (pp) REVERT: P 233 MET cc_start: 0.7566 (ttt) cc_final: 0.7306 (tpp) REVERT: P 242 ASN cc_start: 0.9048 (t0) cc_final: 0.8508 (p0) REVERT: P 275 LEU cc_start: 0.9311 (mt) cc_final: 0.9074 (mt) REVERT: R 12 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: R 86 MET cc_start: 0.8466 (mtm) cc_final: 0.8237 (mtm) REVERT: R 275 LEU cc_start: 0.9207 (tp) cc_final: 0.8988 (tp) REVERT: R 321 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8745 (mm) outliers start: 168 outliers final: 108 residues processed: 624 average time/residue: 0.4210 time to fit residues: 457.3428 Evaluate side-chains 559 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 432 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 348 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 233 MET Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 187 GLU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 350 LYS Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 206 ASP Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 315 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 558 optimal weight: 1.9990 chunk 424 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 566 optimal weight: 3.9990 chunk 600 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 537 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN D 150 GLN D 262 HIS ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 HIS I 160 ASN I 185 HIS ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 262 HIS ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 ASN Q 223 HIS N 262 HIS ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 ASN R 223 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 48936 Z= 0.429 Angle : 0.722 13.915 66669 Z= 0.364 Chirality : 0.044 0.184 7674 Planarity : 0.005 0.050 8529 Dihedral : 5.720 59.248 6873 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 4.97 % Allowed : 14.39 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.48 (0.11), residues: 6093 helix: 1.09 (0.08), residues: 3903 sheet: None (None), residues: 0 loop : -1.05 (0.14), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 345 HIS 0.012 0.001 HIS K 262 PHE 0.028 0.003 PHE N 68 TYR 0.025 0.002 TYR F 157 ARG 0.005 0.001 ARG D 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 429 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 350 LYS cc_start: 0.9243 (tppt) cc_final: 0.8841 (tttt) REVERT: B 85 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9030 (tmm) REVERT: B 94 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.5917 (t-90) REVERT: B 126 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8835 (p) REVERT: B 135 MET cc_start: 0.8287 (mtm) cc_final: 0.8001 (mtm) REVERT: C 198 MET cc_start: 0.8697 (tpp) cc_final: 0.8247 (tpp) REVERT: D 11 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9007 (tt) REVERT: D 94 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.8065 (t-90) REVERT: D 147 ASP cc_start: 0.8141 (p0) cc_final: 0.7889 (p0) REVERT: G 204 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8957 (pp) REVERT: H 12 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: H 350 LYS cc_start: 0.9106 (tptt) cc_final: 0.8806 (tptp) REVERT: E 348 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8415 (t-90) REVERT: E 350 LYS cc_start: 0.9194 (tppt) cc_final: 0.8919 (tttt) REVERT: I 85 MET cc_start: 0.9282 (ppp) cc_final: 0.8879 (ppp) REVERT: I 94 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6161 (t-90) REVERT: I 325 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (tptt) REVERT: I 350 LYS cc_start: 0.8800 (tptp) cc_final: 0.8477 (tptm) REVERT: K 198 MET cc_start: 0.8769 (tpp) cc_final: 0.8513 (tpp) REVERT: M 94 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.7748 (t-90) REVERT: M 147 ASP cc_start: 0.8106 (p0) cc_final: 0.7870 (p0) REVERT: M 283 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7813 (m-10) REVERT: O 206 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: Q 12 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: F 53 LEU cc_start: 0.9173 (tp) cc_final: 0.8964 (tt) REVERT: F 198 MET cc_start: 0.8444 (mmm) cc_final: 0.8129 (mmm) REVERT: J 94 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.5915 (t-90) REVERT: J 100 GLN cc_start: 0.9206 (tt0) cc_final: 0.8760 (tp40) REVERT: J 160 ASN cc_start: 0.8688 (t0) cc_final: 0.8462 (t0) REVERT: J 350 LYS cc_start: 0.8831 (tptp) cc_final: 0.8504 (tptm) REVERT: L 246 TYR cc_start: 0.6364 (t80) cc_final: 0.6161 (t80) REVERT: N 94 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7861 (t-90) REVERT: N 147 ASP cc_start: 0.8209 (p0) cc_final: 0.7963 (p0) REVERT: N 314 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7753 (p0) REVERT: P 204 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8884 (pp) REVERT: P 233 MET cc_start: 0.7555 (ttt) cc_final: 0.7333 (tpp) REVERT: P 242 ASN cc_start: 0.9002 (t0) cc_final: 0.8419 (p0) REVERT: P 352 GLN cc_start: 0.8737 (tp40) cc_final: 0.8495 (tp40) REVERT: R 12 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: R 275 LEU cc_start: 0.9241 (tp) cc_final: 0.9037 (tp) REVERT: R 321 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (mm) outliers start: 237 outliers final: 163 residues processed: 631 average time/residue: 0.4262 time to fit residues: 471.1291 Evaluate side-chains 579 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 395 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain H residue 339 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 348 HIS Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 230 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 HIS Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 283 PHE Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 346 LEU Chi-restraints excluded: chain M residue 351 GLU Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 217 THR Chi-restraints excluded: chain O residue 334 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain O residue 350 LYS Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 160 ASN Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 315 VAL Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 339 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 499 optimal weight: 0.2980 chunk 340 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 446 optimal weight: 20.0000 chunk 247 optimal weight: 0.7980 chunk 512 optimal weight: 0.9990 chunk 414 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 306 optimal weight: 0.8980 chunk 538 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 185 HIS G 160 ASN G 242 ASN ** E 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 160 ASN ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN F 281 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48936 Z= 0.167 Angle : 0.586 13.455 66669 Z= 0.291 Chirality : 0.039 0.155 7674 Planarity : 0.004 0.043 8529 Dihedral : 5.338 59.967 6871 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 4.05 % Allowed : 15.73 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.83 (0.11), residues: 6093 helix: 1.39 (0.08), residues: 3900 sheet: None (None), residues: 0 loop : -0.96 (0.14), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 349 HIS 0.015 0.001 HIS L 262 PHE 0.019 0.001 PHE C 7 TYR 0.021 0.001 TYR N 265 ARG 0.004 0.000 ARG L 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 445 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7958 (tp30) cc_final: 0.7562 (tp30) REVERT: A 321 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8572 (mm) REVERT: B 94 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5862 (t-90) REVERT: B 126 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 135 MET cc_start: 0.8393 (mtm) cc_final: 0.8174 (mtm) REVERT: B 271 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7103 (pmt-80) REVERT: B 350 LYS cc_start: 0.8836 (tptp) cc_final: 0.8511 (tppp) REVERT: C 198 MET cc_start: 0.8696 (tpp) cc_final: 0.8241 (tpp) REVERT: C 228 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7585 (tm-30) REVERT: C 246 TYR cc_start: 0.6184 (t80) cc_final: 0.5537 (t80) REVERT: D 11 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8987 (tt) REVERT: D 27 GLN cc_start: 0.8164 (pm20) cc_final: 0.7806 (pp30) REVERT: D 94 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.8013 (t-90) REVERT: D 147 ASP cc_start: 0.8036 (p0) cc_final: 0.7794 (p0) REVERT: G 204 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8666 (pp) REVERT: H 12 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: H 350 LYS cc_start: 0.8951 (tptt) cc_final: 0.8640 (tptp) REVERT: E 195 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7918 (t80) REVERT: I 85 MET cc_start: 0.9384 (ppp) cc_final: 0.9032 (tmm) REVERT: I 92 SER cc_start: 0.8443 (p) cc_final: 0.8171 (p) REVERT: I 94 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.5710 (t-90) REVERT: I 164 MET cc_start: 0.8781 (tpt) cc_final: 0.8485 (tpp) REVERT: I 325 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8600 (tptt) REVERT: I 350 LYS cc_start: 0.8828 (tptp) cc_final: 0.8489 (tptm) REVERT: K 198 MET cc_start: 0.8656 (tpp) cc_final: 0.8390 (tpp) REVERT: K 372 ASP cc_start: 0.7792 (t0) cc_final: 0.7550 (t0) REVERT: M 94 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: M 147 ASP cc_start: 0.8072 (p0) cc_final: 0.7825 (p0) REVERT: O 206 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: Q 12 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: Q 346 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9093 (mm) REVERT: F 187 GLU cc_start: 0.7616 (tp30) cc_final: 0.7411 (tp30) REVERT: F 350 LYS cc_start: 0.9331 (tppt) cc_final: 0.8900 (tttt) REVERT: J 85 MET cc_start: 0.9290 (ppp) cc_final: 0.9059 (ppp) REVERT: J 94 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.5658 (t-90) REVERT: J 100 GLN cc_start: 0.9084 (tt0) cc_final: 0.8706 (tp40) REVERT: J 160 ASN cc_start: 0.8611 (t0) cc_final: 0.8393 (t0) REVERT: J 350 LYS cc_start: 0.8820 (tptp) cc_final: 0.8579 (tptm) REVERT: L 198 MET cc_start: 0.8690 (tpp) cc_final: 0.8357 (tpp) REVERT: L 246 TYR cc_start: 0.6501 (t80) cc_final: 0.5920 (t80) REVERT: N 27 GLN cc_start: 0.8164 (pm20) cc_final: 0.7817 (pp30) REVERT: N 94 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: N 147 ASP cc_start: 0.8141 (p0) cc_final: 0.7904 (p0) REVERT: N 314 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7632 (p0) REVERT: P 162 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9006 (mm) REVERT: P 204 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8652 (pp) REVERT: P 233 MET cc_start: 0.7553 (ttt) cc_final: 0.6742 (tpp) REVERT: P 242 ASN cc_start: 0.8981 (t0) cc_final: 0.8398 (p0) REVERT: R 12 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: R 275 LEU cc_start: 0.9182 (tp) cc_final: 0.8935 (tp) REVERT: R 321 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8480 (mm) outliers start: 193 outliers final: 117 residues processed: 610 average time/residue: 0.4352 time to fit residues: 459.8437 Evaluate side-chains 556 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 417 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 271 ARG Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 346 LEU Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 334 THR Chi-restraints excluded: chain O residue 350 LYS Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 227 ASN Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 315 VAL Chi-restraints excluded: chain P residue 334 THR Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 201 optimal weight: 0.9990 chunk 540 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 352 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 600 optimal weight: 6.9990 chunk 498 optimal weight: 0.9980 chunk 278 optimal weight: 0.7980 chunk 49 optimal weight: 0.0000 chunk 198 optimal weight: 0.0050 chunk 315 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN E 276 GLN M 150 GLN F 281 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 48936 Z= 0.147 Angle : 0.576 13.579 66669 Z= 0.281 Chirality : 0.038 0.232 7674 Planarity : 0.004 0.042 8529 Dihedral : 5.091 59.811 6869 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 3.88 % Allowed : 16.26 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.95 (0.11), residues: 6093 helix: 1.47 (0.08), residues: 3903 sheet: None (None), residues: 0 loop : -0.89 (0.14), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 349 HIS 0.035 0.001 HIS B 185 PHE 0.018 0.001 PHE C 7 TYR 0.017 0.001 TYR A 157 ARG 0.003 0.000 ARG L 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 479 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 350 LYS cc_start: 0.9219 (tppt) cc_final: 0.8795 (tttt) REVERT: B 85 MET cc_start: 0.9334 (ppp) cc_final: 0.8893 (tmm) REVERT: B 94 HIS cc_start: 0.6354 (OUTLIER) cc_final: 0.5847 (t-90) REVERT: B 126 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 135 MET cc_start: 0.8374 (mtm) cc_final: 0.8087 (mtm) REVERT: B 146 ASN cc_start: 0.8357 (m-40) cc_final: 0.8141 (m-40) REVERT: B 350 LYS cc_start: 0.8781 (tptp) cc_final: 0.8387 (tptp) REVERT: D 11 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8935 (tt) REVERT: D 94 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.8047 (t-90) REVERT: D 147 ASP cc_start: 0.8066 (p0) cc_final: 0.7856 (p0) REVERT: G 150 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: G 242 ASN cc_start: 0.8861 (t160) cc_final: 0.8485 (p0) REVERT: H 12 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: E 241 GLU cc_start: 0.9282 (pm20) cc_final: 0.9058 (pm20) REVERT: E 350 LYS cc_start: 0.9217 (tppt) cc_final: 0.8865 (tmtt) REVERT: I 85 MET cc_start: 0.9398 (ppp) cc_final: 0.9088 (tmm) REVERT: I 92 SER cc_start: 0.8423 (p) cc_final: 0.8131 (p) REVERT: I 94 HIS cc_start: 0.6347 (OUTLIER) cc_final: 0.5686 (t-90) REVERT: I 164 MET cc_start: 0.8666 (tpt) cc_final: 0.8462 (tpp) REVERT: I 325 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (tptt) REVERT: I 350 LYS cc_start: 0.8833 (tptp) cc_final: 0.8469 (tptm) REVERT: K 281 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8734 (tm-30) REVERT: K 372 ASP cc_start: 0.7813 (t0) cc_final: 0.7598 (t0) REVERT: M 94 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: M 147 ASP cc_start: 0.8042 (p0) cc_final: 0.7777 (p0) REVERT: O 206 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: O 242 ASN cc_start: 0.8957 (t0) cc_final: 0.8527 (p0) REVERT: Q 12 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: Q 321 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8680 (mm) REVERT: Q 346 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9100 (mm) REVERT: F 350 LYS cc_start: 0.9366 (tppt) cc_final: 0.8896 (tttt) REVERT: J 85 MET cc_start: 0.9309 (ppp) cc_final: 0.9045 (ppp) REVERT: J 92 SER cc_start: 0.8556 (p) cc_final: 0.8307 (p) REVERT: J 94 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5430 (t-90) REVERT: J 100 GLN cc_start: 0.9054 (tt0) cc_final: 0.8705 (tp40) REVERT: J 160 ASN cc_start: 0.8568 (t0) cc_final: 0.8333 (t0) REVERT: J 350 LYS cc_start: 0.8801 (tptp) cc_final: 0.8559 (tptm) REVERT: L 198 MET cc_start: 0.8680 (tpp) cc_final: 0.8343 (tpp) REVERT: L 246 TYR cc_start: 0.6514 (t80) cc_final: 0.5904 (t80) REVERT: L 281 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8733 (tm-30) REVERT: N 27 GLN cc_start: 0.8045 (pm20) cc_final: 0.7619 (pp30) REVERT: N 94 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7766 (t-90) REVERT: N 147 ASP cc_start: 0.8077 (p0) cc_final: 0.7851 (p0) REVERT: N 233 MET cc_start: 0.7970 (ttm) cc_final: 0.7713 (ttm) REVERT: N 314 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7435 (p0) REVERT: P 204 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8544 (pp) REVERT: P 233 MET cc_start: 0.7516 (ttt) cc_final: 0.6756 (tpp) REVERT: R 12 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: R 86 MET cc_start: 0.8301 (mtm) cc_final: 0.8068 (mtm) REVERT: R 87 LYS cc_start: 0.9148 (tppt) cc_final: 0.8787 (mmtp) REVERT: R 97 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8066 (t0) REVERT: R 275 LEU cc_start: 0.9151 (tp) cc_final: 0.8910 (tp) REVERT: R 321 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8596 (mm) outliers start: 185 outliers final: 119 residues processed: 636 average time/residue: 0.4256 time to fit residues: 468.8182 Evaluate side-chains 574 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 434 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 271 ARG Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 321 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 579 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 438 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 598 optimal weight: 5.9990 chunk 374 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 160 ASN B 185 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** E 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS M 150 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 ASN P 242 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 48936 Z= 0.405 Angle : 0.697 15.065 66669 Z= 0.350 Chirality : 0.042 0.213 7674 Planarity : 0.005 0.042 8529 Dihedral : 5.430 57.562 6866 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 4.47 % Allowed : 16.59 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.67 (0.11), residues: 6093 helix: 1.24 (0.08), residues: 3912 sheet: None (None), residues: 0 loop : -1.00 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 56 HIS 0.022 0.001 HIS E 348 PHE 0.025 0.002 PHE M 139 TYR 0.025 0.002 TYR F 157 ARG 0.025 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 424 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8010 (tp30) cc_final: 0.7640 (tp30) REVERT: A 321 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8611 (mm) REVERT: B 85 MET cc_start: 0.9285 (ppp) cc_final: 0.9010 (tmm) REVERT: B 94 HIS cc_start: 0.6539 (OUTLIER) cc_final: 0.6007 (t-90) REVERT: B 126 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8697 (p) REVERT: B 135 MET cc_start: 0.8322 (mtm) cc_final: 0.8006 (mtm) REVERT: C 372 ASP cc_start: 0.7624 (t0) cc_final: 0.7413 (t0) REVERT: D 11 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8985 (tt) REVERT: D 94 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8069 (t-90) REVERT: D 147 ASP cc_start: 0.8091 (p0) cc_final: 0.7850 (p0) REVERT: D 162 LEU cc_start: 0.9646 (OUTLIER) cc_final: 0.9431 (mm) REVERT: G 242 ASN cc_start: 0.9037 (t0) cc_final: 0.8406 (p0) REVERT: H 12 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: H 350 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8684 (tptt) REVERT: E 350 LYS cc_start: 0.9287 (tppt) cc_final: 0.8892 (tttt) REVERT: E 352 GLN cc_start: 0.7939 (mt0) cc_final: 0.7697 (mt0) REVERT: I 85 MET cc_start: 0.9323 (ppp) cc_final: 0.8914 (ppp) REVERT: I 94 HIS cc_start: 0.6734 (OUTLIER) cc_final: 0.5987 (t-90) REVERT: I 325 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8623 (tptt) REVERT: I 350 LYS cc_start: 0.8862 (tptp) cc_final: 0.8535 (tptm) REVERT: M 94 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7790 (t-90) REVERT: M 147 ASP cc_start: 0.8050 (p0) cc_final: 0.7755 (p0) REVERT: O 206 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: O 242 ASN cc_start: 0.8913 (t0) cc_final: 0.8448 (p0) REVERT: Q 12 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: Q 346 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9111 (mm) REVERT: F 53 LEU cc_start: 0.9189 (tp) cc_final: 0.8965 (tt) REVERT: F 348 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8439 (t-90) REVERT: F 352 GLN cc_start: 0.8412 (mt0) cc_final: 0.8151 (mt0) REVERT: J 85 MET cc_start: 0.9282 (ppp) cc_final: 0.8977 (ppp) REVERT: J 94 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.5946 (t-90) REVERT: J 100 GLN cc_start: 0.9166 (tt0) cc_final: 0.8705 (tp40) REVERT: J 160 ASN cc_start: 0.8668 (t0) cc_final: 0.8397 (t0) REVERT: J 241 GLU cc_start: 0.6207 (pm20) cc_final: 0.5846 (pm20) REVERT: J 350 LYS cc_start: 0.8807 (tptp) cc_final: 0.8552 (tptm) REVERT: L 346 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8956 (mm) REVERT: N 94 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7766 (t-90) REVERT: N 147 ASP cc_start: 0.8143 (p0) cc_final: 0.7914 (p0) REVERT: N 314 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7767 (p0) REVERT: P 204 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8830 (pp) REVERT: P 233 MET cc_start: 0.7583 (ttt) cc_final: 0.6808 (tpp) REVERT: P 242 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8507 (p0) REVERT: P 352 GLN cc_start: 0.8722 (tp40) cc_final: 0.8430 (tp40) REVERT: R 12 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: R 97 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8151 (t0) REVERT: R 275 LEU cc_start: 0.9209 (tp) cc_final: 0.8951 (tp) REVERT: R 321 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8958 (mm) outliers start: 213 outliers final: 149 residues processed: 599 average time/residue: 0.4318 time to fit residues: 449.5647 Evaluate side-chains 581 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 409 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 271 ARG Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 288 HIS Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 346 LEU Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 160 ASN Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 317 PHE Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 150 GLN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 346 LEU Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 370 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 407 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS D 242 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN M 242 ASN O 160 ASN F 281 GLN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 ASN ** P 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 48936 Z= 0.251 Angle : 0.641 14.436 66669 Z= 0.317 Chirality : 0.040 0.210 7674 Planarity : 0.004 0.043 8529 Dihedral : 5.319 58.846 6864 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 4.15 % Allowed : 17.39 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.72 (0.11), residues: 6093 helix: 1.29 (0.08), residues: 3909 sheet: None (None), residues: 0 loop : -0.99 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.010 0.001 HIS B 185 PHE 0.020 0.001 PHE F 139 TYR 0.021 0.001 TYR F 157 ARG 0.011 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 428 time to evaluate : 4.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8029 (tp30) cc_final: 0.7646 (tp30) REVERT: A 321 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8595 (mm) REVERT: A 350 LYS cc_start: 0.9249 (tppt) cc_final: 0.8688 (tttt) REVERT: B 85 MET cc_start: 0.9314 (ppp) cc_final: 0.8984 (tmm) REVERT: B 94 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5933 (t-90) REVERT: B 126 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 135 MET cc_start: 0.8403 (mtm) cc_final: 0.8189 (mtm) REVERT: B 350 LYS cc_start: 0.8760 (tptp) cc_final: 0.8379 (tptp) REVERT: C 372 ASP cc_start: 0.7661 (t0) cc_final: 0.7441 (t0) REVERT: D 11 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9005 (tt) REVERT: D 94 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7946 (t-90) REVERT: D 147 ASP cc_start: 0.8059 (p0) cc_final: 0.7814 (p0) REVERT: G 144 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8590 (mmtm) REVERT: G 150 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8410 (tm130) REVERT: H 12 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7917 (mm-30) REVERT: H 350 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8642 (tptt) REVERT: E 350 LYS cc_start: 0.9217 (tppt) cc_final: 0.8954 (tttt) REVERT: E 352 GLN cc_start: 0.7949 (mt0) cc_final: 0.7710 (mt0) REVERT: I 85 MET cc_start: 0.9344 (ppp) cc_final: 0.8930 (ppp) REVERT: I 92 SER cc_start: 0.8514 (p) cc_final: 0.8246 (p) REVERT: I 94 HIS cc_start: 0.6657 (OUTLIER) cc_final: 0.5935 (t-90) REVERT: I 325 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8620 (tptt) REVERT: I 350 LYS cc_start: 0.8842 (tptp) cc_final: 0.8478 (tptm) REVERT: M 94 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7868 (t-90) REVERT: M 147 ASP cc_start: 0.8074 (p0) cc_final: 0.7777 (p0) REVERT: O 206 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: Q 12 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: Q 346 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9103 (mm) REVERT: F 53 LEU cc_start: 0.9167 (tp) cc_final: 0.8942 (tt) REVERT: F 71 GLU cc_start: 0.7810 (mp0) cc_final: 0.7516 (mp0) REVERT: J 85 MET cc_start: 0.9292 (ppp) cc_final: 0.8996 (ppp) REVERT: J 94 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5858 (t-90) REVERT: J 100 GLN cc_start: 0.9117 (tt0) cc_final: 0.8706 (tp40) REVERT: J 160 ASN cc_start: 0.8716 (t0) cc_final: 0.8410 (t0) REVERT: J 241 GLU cc_start: 0.6305 (pm20) cc_final: 0.5995 (pm20) REVERT: J 350 LYS cc_start: 0.8769 (tptp) cc_final: 0.8536 (tptm) REVERT: L 198 MET cc_start: 0.8756 (tpp) cc_final: 0.8426 (tpp) REVERT: L 246 TYR cc_start: 0.6174 (t80) cc_final: 0.5648 (t80) REVERT: N 27 GLN cc_start: 0.8227 (pm20) cc_final: 0.7874 (pp30) REVERT: N 94 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7809 (t-90) REVERT: N 147 ASP cc_start: 0.8105 (p0) cc_final: 0.7873 (p0) REVERT: N 233 MET cc_start: 0.8044 (ttm) cc_final: 0.7796 (ttm) REVERT: N 314 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7730 (p0) REVERT: P 204 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8714 (pp) REVERT: P 233 MET cc_start: 0.7612 (ttt) cc_final: 0.6830 (tpp) REVERT: P 352 GLN cc_start: 0.8650 (tp40) cc_final: 0.8347 (tp40) REVERT: R 12 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: R 97 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8145 (t0) REVERT: R 275 LEU cc_start: 0.9195 (tp) cc_final: 0.8926 (tp) REVERT: R 321 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8571 (mm) outliers start: 198 outliers final: 150 residues processed: 593 average time/residue: 0.4345 time to fit residues: 444.1963 Evaluate side-chains 581 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 411 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 283 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 271 ARG Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 288 HIS Chi-restraints excluded: chain K residue 309 LYS Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain K residue 364 ILE Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 346 LEU Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 230 VAL Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 544 optimal weight: 0.6980 chunk 573 optimal weight: 6.9990 chunk 523 optimal weight: 0.0870 chunk 557 optimal weight: 0.8980 chunk 335 optimal weight: 0.8980 chunk 242 optimal weight: 9.9990 chunk 437 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 504 optimal weight: 0.9990 chunk 527 optimal weight: 7.9990 chunk 555 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS D 242 ASN G 242 ASN ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 GLN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN N 242 ASN P 140 GLN P 242 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 48936 Z= 0.160 Angle : 0.613 14.267 66669 Z= 0.300 Chirality : 0.039 0.250 7674 Planarity : 0.004 0.046 8529 Dihedral : 5.108 59.935 6864 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.40 % Allowed : 18.31 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.86 (0.11), residues: 6093 helix: 1.40 (0.08), residues: 3906 sheet: None (None), residues: 0 loop : -0.92 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 349 HIS 0.024 0.001 HIS B 185 PHE 0.016 0.001 PHE F 139 TYR 0.019 0.001 TYR F 157 ARG 0.011 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 448 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7766 (mp0) REVERT: A 187 GLU cc_start: 0.7987 (tp30) cc_final: 0.7572 (tp30) REVERT: A 321 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 350 LYS cc_start: 0.9241 (tppt) cc_final: 0.8665 (tttt) REVERT: B 94 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.5774 (t-90) REVERT: B 126 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 135 MET cc_start: 0.8372 (mtm) cc_final: 0.8162 (mtm) REVERT: B 350 LYS cc_start: 0.8756 (tptp) cc_final: 0.8389 (tptp) REVERT: C 246 TYR cc_start: 0.6196 (t80) cc_final: 0.5649 (t80) REVERT: C 372 ASP cc_start: 0.7632 (t0) cc_final: 0.7391 (t0) REVERT: D 11 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8956 (tt) REVERT: D 94 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: D 147 ASP cc_start: 0.8079 (p0) cc_final: 0.7849 (p0) REVERT: G 150 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: G 242 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8391 (p0) REVERT: H 12 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: I 85 MET cc_start: 0.9369 (ppp) cc_final: 0.8996 (tmm) REVERT: I 92 SER cc_start: 0.8526 (p) cc_final: 0.8287 (p) REVERT: I 94 HIS cc_start: 0.6426 (OUTLIER) cc_final: 0.5766 (t-90) REVERT: I 100 GLN cc_start: 0.9059 (tt0) cc_final: 0.8350 (tt0) REVERT: I 325 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8589 (tptt) REVERT: I 350 LYS cc_start: 0.8817 (tptp) cc_final: 0.8511 (tptm) REVERT: M 94 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: M 147 ASP cc_start: 0.7945 (p0) cc_final: 0.7668 (p0) REVERT: O 206 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: O 242 ASN cc_start: 0.8874 (t0) cc_final: 0.8363 (p0) REVERT: Q 12 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7918 (mm-30) REVERT: Q 346 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9073 (mm) REVERT: J 85 MET cc_start: 0.9314 (ppp) cc_final: 0.9019 (ppp) REVERT: J 94 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.5570 (t-90) REVERT: J 100 GLN cc_start: 0.9057 (tt0) cc_final: 0.8680 (tp40) REVERT: J 160 ASN cc_start: 0.8746 (t0) cc_final: 0.8466 (t0) REVERT: J 241 GLU cc_start: 0.6274 (pm20) cc_final: 0.5985 (pm20) REVERT: J 350 LYS cc_start: 0.8782 (tptp) cc_final: 0.8571 (tptm) REVERT: L 165 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8734 (tt) REVERT: L 198 MET cc_start: 0.8709 (tpp) cc_final: 0.8371 (tpp) REVERT: L 246 TYR cc_start: 0.6346 (t80) cc_final: 0.5806 (t80) REVERT: N 27 GLN cc_start: 0.8112 (pm20) cc_final: 0.7682 (pp30) REVERT: N 94 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7840 (t-90) REVERT: N 96 MET cc_start: 0.7536 (ptt) cc_final: 0.7302 (ptt) REVERT: N 147 ASP cc_start: 0.8071 (p0) cc_final: 0.7842 (p0) REVERT: N 233 MET cc_start: 0.8101 (ttm) cc_final: 0.7881 (ttm) REVERT: N 314 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7639 (p0) REVERT: P 204 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8566 (pp) REVERT: P 233 MET cc_start: 0.7582 (ttt) cc_final: 0.6813 (tpp) REVERT: P 346 LEU cc_start: 0.9256 (mm) cc_final: 0.8963 (mm) REVERT: P 352 GLN cc_start: 0.8618 (tp40) cc_final: 0.8345 (tp40) REVERT: R 12 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: R 87 LYS cc_start: 0.9105 (tppt) cc_final: 0.8740 (mmtp) REVERT: R 97 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8145 (t0) REVERT: R 275 LEU cc_start: 0.9183 (tp) cc_final: 0.8916 (tp) REVERT: R 321 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8515 (mm) outliers start: 162 outliers final: 124 residues processed: 583 average time/residue: 0.4377 time to fit residues: 443.1007 Evaluate side-chains 575 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 429 time to evaluate : 4.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 283 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 309 LYS Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 376 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 164 MET Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 242 ASN Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 366 optimal weight: 0.8980 chunk 589 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 410 optimal weight: 3.9990 chunk 618 optimal weight: 0.9980 chunk 569 optimal weight: 9.9990 chunk 492 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 160 ASN B 185 HIS D 242 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 ASN ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS I 188 HIS ** K 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN N 242 ASN P 242 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 48936 Z= 0.211 Angle : 0.624 14.100 66669 Z= 0.308 Chirality : 0.040 0.199 7674 Planarity : 0.004 0.045 8529 Dihedral : 5.080 59.205 6862 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 3.44 % Allowed : 18.23 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.87 (0.11), residues: 6093 helix: 1.41 (0.08), residues: 3906 sheet: None (None), residues: 0 loop : -0.91 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 349 HIS 0.008 0.001 HIS B 185 PHE 0.021 0.001 PHE K 7 TYR 0.020 0.001 TYR F 157 ARG 0.011 0.000 ARG B 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12186 Ramachandran restraints generated. 6093 Oldfield, 0 Emsley, 6093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 429 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8605 (mm) REVERT: A 350 LYS cc_start: 0.9244 (tppt) cc_final: 0.8681 (tttt) REVERT: B 85 MET cc_start: 0.9295 (ppp) cc_final: 0.8901 (tmm) REVERT: B 94 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.5789 (t-90) REVERT: B 126 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8634 (p) REVERT: B 135 MET cc_start: 0.8377 (mtm) cc_final: 0.8140 (mtm) REVERT: B 350 LYS cc_start: 0.8760 (tptp) cc_final: 0.8386 (tptp) REVERT: C 246 TYR cc_start: 0.6330 (t80) cc_final: 0.5806 (t80) REVERT: D 11 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8952 (tt) REVERT: D 94 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7918 (t-90) REVERT: D 147 ASP cc_start: 0.7996 (p0) cc_final: 0.7765 (p0) REVERT: G 150 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: H 12 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: E 195 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7866 (t80) REVERT: I 85 MET cc_start: 0.9397 (ppp) cc_final: 0.8993 (tmm) REVERT: I 92 SER cc_start: 0.8534 (p) cc_final: 0.8268 (p) REVERT: I 94 HIS cc_start: 0.6470 (OUTLIER) cc_final: 0.5771 (t-90) REVERT: I 325 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8644 (tptt) REVERT: I 350 LYS cc_start: 0.8818 (tptp) cc_final: 0.8522 (tptm) REVERT: M 94 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7856 (t-90) REVERT: M 147 ASP cc_start: 0.7966 (p0) cc_final: 0.7680 (p0) REVERT: O 206 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: O 242 ASN cc_start: 0.8882 (t0) cc_final: 0.8349 (p0) REVERT: Q 12 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: Q 346 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9061 (mm) REVERT: F 53 LEU cc_start: 0.9181 (tp) cc_final: 0.8952 (tt) REVERT: J 85 MET cc_start: 0.9327 (ppp) cc_final: 0.9010 (ppp) REVERT: J 94 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.5678 (t-90) REVERT: J 100 GLN cc_start: 0.9086 (tt0) cc_final: 0.8709 (tp40) REVERT: J 160 ASN cc_start: 0.8776 (t0) cc_final: 0.8482 (t0) REVERT: J 241 GLU cc_start: 0.6439 (pm20) cc_final: 0.6150 (pm20) REVERT: J 350 LYS cc_start: 0.8791 (tptp) cc_final: 0.8488 (tptp) REVERT: L 165 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8789 (tt) REVERT: L 198 MET cc_start: 0.8726 (tpp) cc_final: 0.8395 (tpp) REVERT: L 246 TYR cc_start: 0.6271 (t80) cc_final: 0.5729 (t80) REVERT: N 27 GLN cc_start: 0.8174 (pm20) cc_final: 0.7613 (pp30) REVERT: N 94 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: N 147 ASP cc_start: 0.8073 (p0) cc_final: 0.7859 (p0) REVERT: N 233 MET cc_start: 0.8142 (ttm) cc_final: 0.7924 (ttm) REVERT: N 314 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7689 (p0) REVERT: P 204 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8643 (pp) REVERT: P 233 MET cc_start: 0.7607 (ttt) cc_final: 0.6830 (tpp) REVERT: P 242 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8421 (p0) REVERT: P 352 GLN cc_start: 0.8653 (tp40) cc_final: 0.8380 (tp40) REVERT: R 12 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: R 87 LYS cc_start: 0.9102 (tppt) cc_final: 0.8812 (mmtp) REVERT: R 97 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8176 (t0) REVERT: R 275 LEU cc_start: 0.9196 (tp) cc_final: 0.8926 (tp) REVERT: R 321 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8536 (mm) outliers start: 164 outliers final: 127 residues processed: 563 average time/residue: 0.4320 time to fit residues: 422.8578 Evaluate side-chains 573 residues out of total 5205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 423 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 94 HIS Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 283 PHE Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 150 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 203 THR Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 12 GLU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 246 TYR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 317 PHE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 89 PHE Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ARG Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 185 HIS Chi-restraints excluded: chain I residue 277 ASN Chi-restraints excluded: chain I residue 325 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 309 LYS Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 341 ARG Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 94 HIS Chi-restraints excluded: chain M residue 164 MET Chi-restraints excluded: chain M residue 173 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 315 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 173 VAL Chi-restraints excluded: chain O residue 203 THR Chi-restraints excluded: chain O residue 206 ASP Chi-restraints excluded: chain O residue 339 ILE Chi-restraints excluded: chain O residue 374 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 38 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 70 HIS Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 246 TYR Chi-restraints excluded: chain Q residue 277 ASN Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain J residue 94 HIS Chi-restraints excluded: chain J residue 185 HIS Chi-restraints excluded: chain J residue 277 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 364 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 94 HIS Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 242 ASN Chi-restraints excluded: chain N residue 314 ASN Chi-restraints excluded: chain N residue 315 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 85 MET Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 204 LEU Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 97 ASP Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 246 TYR Chi-restraints excluded: chain R residue 277 ASN Chi-restraints excluded: chain R residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 391 optimal weight: 0.2980 chunk 524 optimal weight: 0.3980 chunk 150 optimal weight: 0.0030 chunk 454 optimal weight: 0.6980 chunk 72 optimal weight: 0.0020 chunk 136 optimal weight: 1.9990 chunk 493 optimal weight: 0.0970 chunk 206 optimal weight: 0.6980 chunk 506 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 185 HIS ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS K 262 HIS M 242 ASN ** O 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 242 ASN P 242 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103624 restraints weight = 154277.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102594 restraints weight = 166017.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103789 restraints weight = 172803.314| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 48936 Z= 0.156 Angle : 0.622 15.311 66669 Z= 0.302 Chirality : 0.039 0.196 7674 Planarity : 0.004 0.047 8529 Dihedral : 4.888 59.208 6858 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 2.75 % Allowed : 19.07 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.92 (0.11), residues: 6093 helix: 1.43 (0.08), residues: 3915 sheet: None (None), residues: 0 loop : -0.88 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 349 HIS 0.024 0.001 HIS I 185 PHE 0.016 0.001 PHE N 337 TYR 0.017 0.001 TYR F 157 ARG 0.011 0.000 ARG B 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8298.53 seconds wall clock time: 145 minutes 55.95 seconds (8755.95 seconds total)