Starting phenix.real_space_refine on Sat Aug 23 13:58:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn8_27556/08_2025/8dn8_27556.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2340 atoms to isotropic. 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 32 5.16 5 C 7084 2.51 5 N 1666 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10638 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'U90': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'U90': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.18 Number of scatterers: 10638 At special positions: 0 Unit cell: (92.88, 98.28, 140.4, 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 32 16.00 O 1856 8.00 N 1666 7.00 C 7084 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: 0.68 Conformation dependent library (CDL) restraints added in 259.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 50.9% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.315A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.677A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.681A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.910A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 4.108A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.691A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.502A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 83 removed outlier: 3.509A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.827A pdb=" N ILE B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.790A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 137 removed outlier: 3.846A pdb=" N ILE B 134 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.764A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.745A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.988A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 192 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.673A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 254 Proline residue: B 235 - end of helix removed outlier: 4.780A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 removed outlier: 4.480A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 4.984A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.825A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 172 " --> pdb=" O LEU C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 172' Processing helix chain 'C' and resid 174 through 191 removed outlier: 3.664A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.779A pdb=" N LYS C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 23 through 44 removed outlier: 5.314A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.571A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.629A pdb=" N LYS D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 51' Processing helix chain 'D' and resid 55 through 88 removed outlier: 3.644A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.990A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.478A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 101 through 129 removed outlier: 3.572A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 165 removed outlier: 4.107A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 4.484A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.715A pdb=" N LEU D 192 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.783A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.596A pdb=" N GLY D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.501A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.776A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 2 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.776A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 3 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.563A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 49 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 212 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N HIS A 215 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 265 removed outlier: 5.441A pdb=" N ILE A 259 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU A 287 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU A 261 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE A 330 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 388 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 371 removed outlier: 6.449A pdb=" N LEU A 349 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TRP A 362 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 347 " --> pdb=" O TRP A 362 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP A 364 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 345 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL A 366 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N TYR A 343 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N ASN A 368 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N GLY A 341 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 311 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 380 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.755A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 283 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 263 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP C 285 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 266 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.591A pdb=" N ARG C 3 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 86 removed outlier: 7.257A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 223 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 274 through 276 removed outlier: 6.648A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 367 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 345 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 274 through 276 removed outlier: 6.648A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 367 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 345 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS C 351 " --> pdb=" O CYS C 359 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYS C 359 " --> pdb=" O LYS C 351 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1377 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: 1.25 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3158 1.34 - 1.46: 1903 1.46 - 1.57: 5803 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 10916 Sorted by residual: bond pdb=" C5' U90 A 501 " pdb=" C6' U90 A 501 " ideal model delta sigma weight residual 1.511 1.412 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C5' U90 A 501 " pdb=" O5' U90 A 501 " ideal model delta sigma weight residual 1.437 1.533 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5' U90 C 501 " pdb=" C6' U90 C 501 " ideal model delta sigma weight residual 1.511 1.415 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C5' U90 C 501 " pdb=" O5' U90 C 501 " ideal model delta sigma weight residual 1.437 1.530 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C2' U90 A 501 " pdb=" C3' U90 A 501 " ideal model delta sigma weight residual 1.526 1.451 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14450 1.88 - 3.75: 265 3.75 - 5.63: 43 5.63 - 7.50: 5 7.50 - 9.38: 1 Bond angle restraints: 14764 Sorted by residual: angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 112.96 108.45 4.51 1.00e+00 1.00e+00 2.04e+01 angle pdb=" CA CYS C 359 " pdb=" C CYS C 359 " pdb=" O CYS C 359 " ideal model delta sigma weight residual 120.92 117.26 3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" N GLN B 12 " pdb=" CA GLN B 12 " pdb=" CB GLN B 12 " ideal model delta sigma weight residual 110.12 115.15 -5.03 1.47e+00 4.63e-01 1.17e+01 angle pdb=" N GLU C 358 " pdb=" CA GLU C 358 " pdb=" C GLU C 358 " ideal model delta sigma weight residual 107.49 113.31 -5.82 1.74e+00 3.30e-01 1.12e+01 angle pdb=" CA PHE C 369 " pdb=" CB PHE C 369 " pdb=" CG PHE C 369 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 ... (remaining 14759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5773 17.85 - 35.71: 542 35.71 - 53.56: 89 53.56 - 71.42: 13 71.42 - 89.27: 5 Dihedral angle restraints: 6422 sinusoidal: 2642 harmonic: 3780 Sorted by residual: dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU C 88 " pdb=" C LEU C 88 " pdb=" N GLU C 89 " pdb=" CA GLU C 89 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA HIS C 187 " pdb=" C HIS C 187 " pdb=" N LYS C 188 " pdb=" CA LYS C 188 " ideal model delta harmonic sigma weight residual -180.00 -163.40 -16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1145 0.039 - 0.079: 366 0.079 - 0.118: 120 0.118 - 0.158: 21 0.158 - 0.197: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA PHE C 369 " pdb=" N PHE C 369 " pdb=" C PHE C 369 " pdb=" CB PHE C 369 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CB ILE B 47 " pdb=" CA ILE B 47 " pdb=" CG1 ILE B 47 " pdb=" CG2 ILE B 47 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CA MET B 156 " pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CB MET B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1653 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 367 " 0.016 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C CYS C 367 " -0.053 2.00e-02 2.50e+03 pdb=" O CYS C 367 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN C 368 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 152 " 0.015 2.00e-02 2.50e+03 1.57e-02 4.31e+00 pdb=" CG PHE D 152 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 152 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 152 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 152 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 152 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 358 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C GLU C 358 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU C 358 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS C 359 " -0.011 2.00e-02 2.50e+03 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.25: 10755 3.25 - 3.80: 16722 3.80 - 4.35: 20497 4.35 - 4.90: 35009 Nonbonded interactions: 83259 Sorted by model distance: nonbonded pdb=" OD1 ASP C 303 " pdb=" N ARG C 304 " model vdw 2.157 3.120 nonbonded pdb=" O GLU C 226 " pdb=" NE2 GLN C 230 " model vdw 2.201 3.120 nonbonded pdb=" O PHE A 134 " pdb=" OH TYR A 142 " model vdw 2.205 3.040 nonbonded pdb=" O THR A 246 " pdb=" ND2 ASN A 250 " model vdw 2.266 3.120 nonbonded pdb=" OH TYR D 60 " pdb=" O VAL D 186 " model vdw 2.266 3.040 ... (remaining 83254 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.930 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.004 0.099 10916 Z= 0.212 Angle : 0.619 9.381 14764 Z= 0.344 Chirality : 0.044 0.197 1656 Planarity : 0.003 0.030 1814 Dihedral : 13.760 89.269 4006 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.24), residues: 1292 helix: 1.11 (0.22), residues: 611 sheet: -0.14 (0.43), residues: 164 loop : -1.56 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 263 TYR 0.018 0.001 TYR B 206 PHE 0.036 0.001 PHE D 152 TRP 0.020 0.002 TRP D 31 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00426 (10916) covalent geometry : angle 0.61918 (14764) hydrogen bonds : bond 0.14665 ( 467) hydrogen bonds : angle 5.96116 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.304 Fit side-chains REVERT: A 147 ILE cc_start: 0.9104 (mm) cc_final: 0.8782 (tp) REVERT: A 252 TYR cc_start: 0.7409 (m-80) cc_final: 0.7071 (m-80) REVERT: B 56 THR cc_start: 0.8424 (m) cc_final: 0.8030 (p) REVERT: B 167 ASP cc_start: 0.8386 (p0) cc_final: 0.7250 (p0) REVERT: C 201 MET cc_start: 0.7935 (mmp) cc_final: 0.7709 (mmm) REVERT: D 156 MET cc_start: 0.8257 (mpp) cc_final: 0.7939 (mpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.0786 time to fit residues: 26.9202 Evaluate side-chains 170 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 361 HIS B 113 ASN C 215 HIS C 230 GLN C 307 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114198 restraints weight = 20674.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116273 restraints weight = 12330.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117139 restraints weight = 8622.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117450 restraints weight = 7843.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117694 restraints weight = 7564.512| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10916 Z= 0.208 Angle : 0.639 10.295 14764 Z= 0.330 Chirality : 0.044 0.149 1656 Planarity : 0.004 0.044 1814 Dihedral : 4.357 29.767 1448 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.24), residues: 1292 helix: 0.77 (0.21), residues: 630 sheet: -0.28 (0.42), residues: 168 loop : -1.50 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 17 TYR 0.017 0.001 TYR B 206 PHE 0.033 0.002 PHE C 152 TRP 0.015 0.002 TRP C 8 HIS 0.006 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00498 (10916) covalent geometry : angle 0.63895 (14764) hydrogen bonds : bond 0.04740 ( 467) hydrogen bonds : angle 4.85291 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9147 (mm) cc_final: 0.8905 (tp) REVERT: A 252 TYR cc_start: 0.7236 (m-80) cc_final: 0.6961 (m-80) REVERT: A 350 HIS cc_start: 0.4725 (p90) cc_final: 0.4366 (p90) REVERT: B 56 THR cc_start: 0.8499 (m) cc_final: 0.8108 (p) REVERT: C 127 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: C 157 HIS cc_start: 0.7893 (m-70) cc_final: 0.7496 (t-90) REVERT: C 177 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7575 (tp-100) REVERT: C 201 MET cc_start: 0.7619 (mmp) cc_final: 0.7384 (mmm) REVERT: C 236 MET cc_start: 0.7055 (ppp) cc_final: 0.6665 (tmm) REVERT: C 261 GLU cc_start: 0.6773 (pp20) cc_final: 0.6515 (pp20) REVERT: D 8 GLU cc_start: 0.8241 (tp30) cc_final: 0.7959 (tp30) REVERT: D 12 GLN cc_start: 0.8233 (pt0) cc_final: 0.7882 (pt0) REVERT: D 13 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8401 (tm-30) REVERT: D 20 ASP cc_start: 0.6565 (p0) cc_final: 0.6028 (t0) REVERT: D 145 TYR cc_start: 0.8431 (t80) cc_final: 0.8220 (t80) REVERT: D 152 PHE cc_start: 0.8168 (t80) cc_final: 0.7868 (t80) REVERT: D 156 MET cc_start: 0.8272 (mpp) cc_final: 0.7561 (mpp) outliers start: 26 outliers final: 17 residues processed: 204 average time/residue: 0.0839 time to fit residues: 24.8726 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 96 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095072 restraints weight = 20534.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096273 restraints weight = 14715.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097633 restraints weight = 10251.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097706 restraints weight = 9142.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098063 restraints weight = 9273.741| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10916 Z= 0.154 Angle : 0.604 13.252 14764 Z= 0.308 Chirality : 0.042 0.135 1656 Planarity : 0.003 0.029 1814 Dihedral : 4.224 23.839 1448 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.41 % Allowed : 14.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.24), residues: 1292 helix: 0.89 (0.22), residues: 621 sheet: -0.06 (0.44), residues: 161 loop : -1.51 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 80 TYR 0.019 0.001 TYR B 206 PHE 0.023 0.001 PHE C 152 TRP 0.015 0.002 TRP B 71 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00367 (10916) covalent geometry : angle 0.60380 (14764) hydrogen bonds : bond 0.04291 ( 467) hydrogen bonds : angle 4.67479 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 PHE cc_start: 0.7505 (m-10) cc_final: 0.7258 (m-10) REVERT: C 20 ARG cc_start: 0.8553 (mtt90) cc_final: 0.8242 (mtt-85) REVERT: C 127 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: C 157 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7492 (t-90) REVERT: C 177 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7761 (tp-100) REVERT: C 201 MET cc_start: 0.7643 (mmp) cc_final: 0.7385 (mmm) REVERT: C 261 GLU cc_start: 0.6808 (pp20) cc_final: 0.6534 (pp20) REVERT: D 8 GLU cc_start: 0.8334 (tp30) cc_final: 0.8014 (tp30) REVERT: D 12 GLN cc_start: 0.8167 (pt0) cc_final: 0.7826 (pt0) REVERT: D 20 ASP cc_start: 0.6588 (p0) cc_final: 0.6059 (t0) REVERT: D 156 MET cc_start: 0.8328 (mpp) cc_final: 0.7911 (mpp) REVERT: D 249 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7365 (mm-30) outliers start: 28 outliers final: 19 residues processed: 200 average time/residue: 0.0854 time to fit residues: 24.7668 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.0070 chunk 41 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095230 restraints weight = 20608.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095749 restraints weight = 12124.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095642 restraints weight = 9397.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096667 restraints weight = 10028.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096470 restraints weight = 8769.017| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10916 Z= 0.189 Angle : 0.614 9.033 14764 Z= 0.315 Chirality : 0.043 0.134 1656 Planarity : 0.003 0.030 1814 Dihedral : 4.256 20.913 1448 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.71 % Allowed : 16.47 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1292 helix: 0.78 (0.21), residues: 628 sheet: 0.03 (0.42), residues: 172 loop : -1.53 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 392 TYR 0.017 0.001 TYR B 206 PHE 0.019 0.002 PHE C 152 TRP 0.035 0.002 TRP B 26 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00455 (10916) covalent geometry : angle 0.61403 (14764) hydrogen bonds : bond 0.04426 ( 467) hydrogen bonds : angle 4.61545 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 HIS cc_start: 0.4713 (p-80) cc_final: 0.4430 (p-80) REVERT: B 8 GLU cc_start: 0.9222 (tt0) cc_final: 0.8965 (tt0) REVERT: C 20 ARG cc_start: 0.8529 (mtt90) cc_final: 0.8224 (mtt-85) REVERT: C 101 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 157 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7563 (t-90) REVERT: C 177 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7975 (tp-100) REVERT: C 201 MET cc_start: 0.7798 (mmp) cc_final: 0.7533 (mmm) REVERT: C 236 MET cc_start: 0.7156 (ppp) cc_final: 0.6902 (tmm) REVERT: C 261 GLU cc_start: 0.7064 (pp20) cc_final: 0.6670 (pp20) REVERT: D 20 ASP cc_start: 0.6671 (p0) cc_final: 0.6055 (t0) REVERT: D 156 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8056 (mpp) REVERT: D 246 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8634 (mmmt) REVERT: D 249 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 43 outliers final: 29 residues processed: 206 average time/residue: 0.0811 time to fit residues: 24.6307 Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 188 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102728 restraints weight = 20250.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106057 restraints weight = 11481.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106875 restraints weight = 8933.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108489 restraints weight = 7126.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108518 restraints weight = 7113.246| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 10916 Z= 0.331 Angle : 0.729 8.653 14764 Z= 0.376 Chirality : 0.046 0.132 1656 Planarity : 0.004 0.035 1814 Dihedral : 4.558 20.391 1448 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.74 % Allowed : 18.36 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.23), residues: 1292 helix: 0.42 (0.21), residues: 628 sheet: -0.32 (0.42), residues: 173 loop : -1.72 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 263 TYR 0.033 0.002 TYR C 142 PHE 0.019 0.002 PHE D 74 TRP 0.020 0.002 TRP B 26 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00791 (10916) covalent geometry : angle 0.72919 (14764) hydrogen bonds : bond 0.05472 ( 467) hydrogen bonds : angle 4.96152 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9227 (mm) cc_final: 0.8927 (tp) REVERT: A 264 LEU cc_start: 0.8235 (pt) cc_final: 0.7893 (pt) REVERT: A 274 PHE cc_start: 0.7640 (m-10) cc_final: 0.7355 (m-10) REVERT: A 350 HIS cc_start: 0.5423 (p-80) cc_final: 0.4960 (p-80) REVERT: C 20 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8320 (mtt-85) REVERT: C 101 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8398 (mt) REVERT: C 127 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: C 157 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7595 (t-90) REVERT: C 177 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8123 (tp-100) REVERT: C 236 MET cc_start: 0.7270 (ppp) cc_final: 0.7017 (tmm) REVERT: C 261 GLU cc_start: 0.7171 (pp20) cc_final: 0.6906 (pp20) REVERT: C 267 GLU cc_start: 0.7742 (mp0) cc_final: 0.7416 (mp0) REVERT: C 331 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7538 (p) REVERT: C 361 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7446 (t70) REVERT: D 20 ASP cc_start: 0.6567 (p0) cc_final: 0.5989 (t0) REVERT: D 156 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8120 (mpp) outliers start: 55 outliers final: 39 residues processed: 207 average time/residue: 0.0841 time to fit residues: 25.7214 Evaluate side-chains 197 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 177 GLN ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.156762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112468 restraints weight = 20842.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113617 restraints weight = 12774.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.114971 restraints weight = 8943.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116243 restraints weight = 7727.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116160 restraints weight = 7338.910| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10916 Z= 0.164 Angle : 0.614 8.088 14764 Z= 0.318 Chirality : 0.042 0.135 1656 Planarity : 0.003 0.036 1814 Dihedral : 4.353 19.445 1448 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.79 % Allowed : 20.78 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.24), residues: 1292 helix: 0.65 (0.21), residues: 626 sheet: -0.24 (0.42), residues: 174 loop : -1.63 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.025 0.001 TYR A 252 PHE 0.024 0.001 PHE D 152 TRP 0.018 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00392 (10916) covalent geometry : angle 0.61414 (14764) hydrogen bonds : bond 0.04469 ( 467) hydrogen bonds : angle 4.66022 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8111 (pt) cc_final: 0.7807 (pt) REVERT: A 274 PHE cc_start: 0.7693 (m-10) cc_final: 0.7446 (m-10) REVERT: A 334 MET cc_start: 0.8348 (mmm) cc_final: 0.8036 (mmm) REVERT: A 350 HIS cc_start: 0.5474 (p-80) cc_final: 0.5135 (p-80) REVERT: B 8 GLU cc_start: 0.8913 (tt0) cc_final: 0.8684 (tp30) REVERT: C 20 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8301 (mtt-85) REVERT: C 101 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8254 (mp) REVERT: C 127 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: C 157 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: C 236 MET cc_start: 0.7374 (ppp) cc_final: 0.7031 (tmm) REVERT: C 261 GLU cc_start: 0.6953 (pp20) cc_final: 0.6714 (pp20) REVERT: C 267 GLU cc_start: 0.7792 (mp0) cc_final: 0.7494 (mp0) REVERT: C 357 GLN cc_start: 0.8045 (mt0) cc_final: 0.7679 (tm-30) REVERT: C 361 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.7354 (t70) REVERT: D 20 ASP cc_start: 0.6486 (p0) cc_final: 0.5878 (t0) REVERT: D 156 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8161 (mpp) REVERT: D 249 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7425 (mm-30) outliers start: 44 outliers final: 30 residues processed: 205 average time/residue: 0.0798 time to fit residues: 24.0772 Evaluate side-chains 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 239 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.152126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103520 restraints weight = 20132.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107466 restraints weight = 10876.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109814 restraints weight = 7715.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111374 restraints weight = 6373.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112070 restraints weight = 5698.471| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10916 Z= 0.243 Angle : 0.665 8.063 14764 Z= 0.344 Chirality : 0.044 0.134 1656 Planarity : 0.004 0.038 1814 Dihedral : 4.418 19.932 1448 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.66 % Allowed : 20.95 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1292 helix: 0.57 (0.21), residues: 626 sheet: -0.44 (0.42), residues: 176 loop : -1.67 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 263 TYR 0.024 0.002 TYR B 206 PHE 0.024 0.002 PHE C 94 TRP 0.017 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00582 (10916) covalent geometry : angle 0.66544 (14764) hydrogen bonds : bond 0.04915 ( 467) hydrogen bonds : angle 4.76903 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8517 (m-80) cc_final: 0.8104 (m-80) REVERT: A 147 ILE cc_start: 0.9198 (mm) cc_final: 0.8821 (tp) REVERT: A 207 LEU cc_start: 0.8243 (tp) cc_final: 0.8014 (pp) REVERT: A 264 LEU cc_start: 0.8004 (pt) cc_final: 0.7721 (pt) REVERT: A 274 PHE cc_start: 0.7776 (m-10) cc_final: 0.7515 (m-10) REVERT: A 350 HIS cc_start: 0.5558 (p-80) cc_final: 0.5078 (p-80) REVERT: B 11 ARG cc_start: 0.8935 (ttm170) cc_final: 0.8585 (ttm170) REVERT: B 12 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: C 20 ARG cc_start: 0.8625 (mtt90) cc_final: 0.8356 (mtt-85) REVERT: C 127 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: C 157 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7471 (t-90) REVERT: C 267 GLU cc_start: 0.7775 (mp0) cc_final: 0.7570 (mp0) REVERT: C 357 GLN cc_start: 0.7937 (mt0) cc_final: 0.7569 (tm-30) REVERT: C 361 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7037 (t70) REVERT: D 20 ASP cc_start: 0.6307 (p0) cc_final: 0.5766 (t0) REVERT: D 156 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8219 (mpp) outliers start: 54 outliers final: 43 residues processed: 205 average time/residue: 0.0997 time to fit residues: 30.2327 Evaluate side-chains 205 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 361 HIS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 239 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 76 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.159303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.116621 restraints weight = 20562.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.117563 restraints weight = 11416.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.117875 restraints weight = 7774.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118421 restraints weight = 7502.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118724 restraints weight = 6941.230| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10916 Z= 0.122 Angle : 0.610 9.422 14764 Z= 0.315 Chirality : 0.041 0.135 1656 Planarity : 0.003 0.038 1814 Dihedral : 4.181 18.445 1448 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.10 % Allowed : 23.19 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.24), residues: 1292 helix: 0.84 (0.22), residues: 626 sheet: -0.19 (0.42), residues: 172 loop : -1.55 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 263 TYR 0.019 0.001 TYR B 206 PHE 0.017 0.001 PHE B 195 TRP 0.016 0.002 TRP B 71 HIS 0.005 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00277 (10916) covalent geometry : angle 0.60971 (14764) hydrogen bonds : bond 0.03878 ( 467) hydrogen bonds : angle 4.52425 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9161 (mm) cc_final: 0.8786 (tp) REVERT: A 152 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 350 HIS cc_start: 0.5310 (p-80) cc_final: 0.4854 (p-80) REVERT: B 8 GLU cc_start: 0.8418 (tp30) cc_final: 0.8212 (tp30) REVERT: B 175 PHE cc_start: 0.8260 (t80) cc_final: 0.7853 (t80) REVERT: C 20 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8325 (mtt-85) REVERT: C 127 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8556 (pm20) REVERT: C 157 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7413 (t-90) REVERT: C 267 GLU cc_start: 0.7835 (mp0) cc_final: 0.7586 (mp0) REVERT: C 357 GLN cc_start: 0.7927 (mt0) cc_final: 0.7633 (tm-30) REVERT: D 156 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8159 (mpp) REVERT: D 249 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6428 (mm-30) outliers start: 36 outliers final: 26 residues processed: 204 average time/residue: 0.0990 time to fit residues: 29.9012 Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 239 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.151282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.102450 restraints weight = 20131.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.106311 restraints weight = 10965.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108721 restraints weight = 7860.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.110244 restraints weight = 6489.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110873 restraints weight = 5818.250| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 10916 Z= 0.283 Angle : 0.728 11.067 14764 Z= 0.373 Chirality : 0.045 0.149 1656 Planarity : 0.004 0.040 1814 Dihedral : 4.443 19.751 1448 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.10 % Allowed : 24.05 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.24), residues: 1292 helix: 0.60 (0.21), residues: 626 sheet: -0.52 (0.42), residues: 174 loop : -1.65 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.023 0.002 TYR B 206 PHE 0.028 0.002 PHE C 181 TRP 0.020 0.002 TRP B 71 HIS 0.004 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00677 (10916) covalent geometry : angle 0.72790 (14764) hydrogen bonds : bond 0.05200 ( 467) hydrogen bonds : angle 4.80685 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 350 HIS cc_start: 0.5734 (p-80) cc_final: 0.5220 (p-80) REVERT: B 156 MET cc_start: 0.8011 (mmm) cc_final: 0.7750 (mtp) REVERT: C 20 ARG cc_start: 0.8675 (mtt90) cc_final: 0.8396 (mtt-85) REVERT: C 127 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: C 157 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7537 (t-90) REVERT: D 156 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8235 (mpp) REVERT: D 249 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6589 (mm-30) outliers start: 36 outliers final: 31 residues processed: 188 average time/residue: 0.0989 time to fit residues: 27.7990 Evaluate side-chains 190 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.153894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106919 restraints weight = 19958.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110933 restraints weight = 10463.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.113509 restraints weight = 7320.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115098 restraints weight = 5964.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115800 restraints weight = 5273.950| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10916 Z= 0.159 Angle : 0.665 10.244 14764 Z= 0.340 Chirality : 0.042 0.134 1656 Planarity : 0.003 0.041 1814 Dihedral : 4.273 19.230 1448 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.93 % Allowed : 24.48 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.24), residues: 1292 helix: 0.71 (0.22), residues: 626 sheet: -0.47 (0.42), residues: 174 loop : -1.53 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 263 TYR 0.019 0.001 TYR B 206 PHE 0.030 0.002 PHE C 181 TRP 0.018 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00378 (10916) covalent geometry : angle 0.66528 (14764) hydrogen bonds : bond 0.04376 ( 467) hydrogen bonds : angle 4.60905 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8485 (m-80) cc_final: 0.8086 (m-80) REVERT: A 152 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8095 (t80) REVERT: A 350 HIS cc_start: 0.5514 (p-80) cc_final: 0.4872 (p90) REVERT: B 8 GLU cc_start: 0.8489 (tp30) cc_final: 0.7857 (tp30) REVERT: C 20 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8418 (mtt-85) REVERT: C 127 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: C 157 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7405 (t-90) REVERT: C 353 MET cc_start: 0.8505 (tpt) cc_final: 0.8167 (tpp) REVERT: C 357 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 156 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8232 (mpp) REVERT: D 249 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6395 (mm-30) outliers start: 34 outliers final: 28 residues processed: 189 average time/residue: 0.0956 time to fit residues: 26.9701 Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 239 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110354 restraints weight = 19987.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114259 restraints weight = 10785.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116709 restraints weight = 7603.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118151 restraints weight = 6224.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.119136 restraints weight = 5530.847| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10916 Z= 0.127 Angle : 0.638 10.560 14764 Z= 0.325 Chirality : 0.041 0.136 1656 Planarity : 0.003 0.039 1814 Dihedral : 4.099 17.980 1448 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.76 % Allowed : 24.57 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1292 helix: 0.86 (0.22), residues: 625 sheet: -0.37 (0.42), residues: 176 loop : -1.45 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 17 TYR 0.013 0.001 TYR A 252 PHE 0.026 0.001 PHE D 175 TRP 0.016 0.002 TRP B 71 HIS 0.006 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00295 (10916) covalent geometry : angle 0.63845 (14764) hydrogen bonds : bond 0.03841 ( 467) hydrogen bonds : angle 4.49132 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.71 seconds wall clock time: 32 minutes 58.15 seconds (1978.15 seconds total)