Starting phenix.real_space_refine on Mon Dec 30 07:13:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn8_27556/12_2024/8dn8_27556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn8_27556/12_2024/8dn8_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_27556/12_2024/8dn8_27556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn8_27556/12_2024/8dn8_27556.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn8_27556/12_2024/8dn8_27556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn8_27556/12_2024/8dn8_27556.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.93, per 1000 atoms: 0.65 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: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.19 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: 3.37 Time building geometry restraints manager: 3.17 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: 0.00 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.180 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- 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= 0.280 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 : 9.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 TRP 0.020 0.002 TRP D 31 HIS 0.003 0.001 HIS A 268 PHE 0.036 0.001 PHE D 152 TYR 0.018 0.001 TYR B 206 ARG 0.011 0.001 ARG C 263 *********************** 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 : 1.376 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: 0.7072 (m-80) REVERT: B 56 THR cc_start: 0.8424 (m) cc_final: 0.8031 (p) REVERT: B 167 ASP cc_start: 0.8386 (p0) cc_final: 0.7465 (p0) REVERT: C 201 MET cc_start: 0.7935 (mmp) cc_final: 0.7708 (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: 0.2163 time to fit residues: 73.0554 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10916 Z= 0.342 Angle : 0.643 10.125 14764 Z= 0.332 Chirality : 0.044 0.157 1656 Planarity : 0.004 0.045 1814 Dihedral : 4.381 31.305 1448 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.24 % Allowed : 11.72 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 630 sheet: -0.17 (0.43), residues: 162 loop : -1.51 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 8 HIS 0.005 0.001 HIS C 175 PHE 0.036 0.002 PHE C 152 TYR 0.017 0.001 TYR B 206 ARG 0.004 0.001 ARG A 116 *********************** 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 207 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.408 Fit side-chains REVERT: A 147 ILE cc_start: 0.9141 (mm) cc_final: 0.8903 (tp) REVERT: A 252 TYR cc_start: 0.7402 (m-80) cc_final: 0.7005 (m-80) REVERT: B 56 THR cc_start: 0.8551 (m) cc_final: 0.8171 (p) REVERT: C 127 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: C 157 HIS cc_start: 0.8011 (m-70) cc_final: 0.7589 (t-90) REVERT: C 177 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7791 (tp-100) REVERT: C 201 MET cc_start: 0.7770 (mmp) cc_final: 0.7513 (mmm) REVERT: C 236 MET cc_start: 0.7063 (ppp) cc_final: 0.6689 (tmm) REVERT: C 261 GLU cc_start: 0.6871 (pp20) cc_final: 0.6619 (pp20) REVERT: D 8 GLU cc_start: 0.8355 (tp30) cc_final: 0.8036 (tp30) REVERT: D 13 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8439 (tm-30) REVERT: D 20 ASP cc_start: 0.6582 (p0) cc_final: 0.6034 (t0) REVERT: D 145 TYR cc_start: 0.8461 (t80) cc_final: 0.8244 (t80) REVERT: D 152 PHE cc_start: 0.8184 (t80) cc_final: 0.7948 (t80) REVERT: D 156 MET cc_start: 0.8238 (mpp) cc_final: 0.7544 (mpp) outliers start: 26 outliers final: 17 residues processed: 201 average time/residue: 0.2138 time to fit residues: 62.9972 Evaluate side-chains 178 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 64 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 0.0030 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 116 optimal weight: 0.0980 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10916 Z= 0.249 Angle : 0.602 14.091 14764 Z= 0.306 Chirality : 0.042 0.135 1656 Planarity : 0.003 0.030 1814 Dihedral : 4.244 23.364 1448 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.67 % Allowed : 14.14 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1292 helix: 0.82 (0.22), residues: 628 sheet: 0.01 (0.44), residues: 155 loop : -1.59 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 71 HIS 0.005 0.001 HIS C 175 PHE 0.025 0.001 PHE C 152 TYR 0.019 0.001 TYR B 206 ARG 0.006 0.001 ARG A 263 *********************** 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 214 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 252 TYR cc_start: 0.7444 (m-80) cc_final: 0.7181 (m-80) REVERT: A 274 PHE cc_start: 0.7306 (m-10) cc_final: 0.7066 (m-10) REVERT: C 20 ARG cc_start: 0.8533 (mtt90) cc_final: 0.8218 (mtt-85) REVERT: C 127 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: C 157 HIS cc_start: 0.7946 (OUTLIER) cc_final: 0.7594 (t-90) REVERT: C 177 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7868 (tp-100) REVERT: C 201 MET cc_start: 0.7802 (mmp) cc_final: 0.7525 (mmm) REVERT: C 261 GLU cc_start: 0.6989 (pp20) cc_final: 0.6693 (pp20) REVERT: D 8 GLU cc_start: 0.8369 (tp30) cc_final: 0.8059 (tp30) REVERT: D 12 GLN cc_start: 0.8132 (pt0) cc_final: 0.7803 (pt0) REVERT: D 20 ASP cc_start: 0.6637 (p0) cc_final: 0.6096 (t0) REVERT: D 156 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7857 (mpp) outliers start: 31 outliers final: 20 residues processed: 203 average time/residue: 0.2404 time to fit residues: 69.9199 Evaluate side-chains 184 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 160 THR 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 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 156 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 115 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2109 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= 0.223 Angle : 0.589 9.721 14764 Z= 0.301 Chirality : 0.042 0.141 1656 Planarity : 0.003 0.030 1814 Dihedral : 4.197 22.396 1448 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.10 % Allowed : 16.72 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1292 helix: 0.87 (0.22), residues: 628 sheet: 0.22 (0.44), residues: 159 loop : -1.57 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 26 HIS 0.007 0.001 HIS A 350 PHE 0.020 0.001 PHE C 152 TYR 0.015 0.001 TYR B 206 ARG 0.006 0.001 ARG A 392 *********************** 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: 36 poor density : 182 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.7482 (m-80) cc_final: 0.7253 (m-80) REVERT: C 20 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8255 (mtt-85) REVERT: C 101 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 127 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: C 157 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7567 (t-90) REVERT: C 177 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7900 (tp-100) REVERT: C 201 MET cc_start: 0.7780 (mmp) cc_final: 0.7520 (mmm) REVERT: C 236 MET cc_start: 0.7251 (ppp) cc_final: 0.6999 (tmm) REVERT: C 261 GLU cc_start: 0.7008 (pp20) cc_final: 0.6731 (pp20) REVERT: D 20 ASP cc_start: 0.6588 (p0) cc_final: 0.5918 (t0) REVERT: D 156 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7778 (mpp) REVERT: D 249 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7065 (mm-30) outliers start: 36 outliers final: 24 residues processed: 207 average time/residue: 0.2218 time to fit residues: 66.6839 Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 9 LEU Chi-restraints excluded: chain B residue 56 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 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 101 LEU 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 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 103 optimal weight: 0.0070 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2345 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= 0.251 Angle : 0.590 9.599 14764 Z= 0.302 Chirality : 0.042 0.135 1656 Planarity : 0.003 0.031 1814 Dihedral : 4.164 20.016 1448 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.28 % Allowed : 18.71 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1292 helix: 0.82 (0.22), residues: 628 sheet: 0.22 (0.44), residues: 158 loop : -1.61 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 26 HIS 0.004 0.001 HIS A 350 PHE 0.021 0.001 PHE B 92 TYR 0.035 0.001 TYR C 142 ARG 0.005 0.000 ARG B 80 *********************** 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 208 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.7484 (m-80) cc_final: 0.7268 (m-80) REVERT: A 264 LEU cc_start: 0.8252 (pt) cc_final: 0.7897 (pt) REVERT: A 274 PHE cc_start: 0.7373 (m-10) cc_final: 0.7100 (m-10) REVERT: C 20 ARG cc_start: 0.8581 (mtt90) cc_final: 0.8268 (mtt-85) REVERT: C 101 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8329 (mt) REVERT: C 157 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7575 (t-90) REVERT: C 177 GLN cc_start: 0.8268 (tp-100) cc_final: 0.8040 (tp-100) REVERT: C 201 MET cc_start: 0.7776 (mmp) cc_final: 0.7517 (mmm) REVERT: C 236 MET cc_start: 0.7038 (ppp) cc_final: 0.6712 (tmm) REVERT: C 261 GLU cc_start: 0.7120 (pp20) cc_final: 0.6823 (pp20) REVERT: C 361 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7463 (t70) REVERT: D 20 ASP cc_start: 0.6647 (p0) cc_final: 0.5978 (t0) REVERT: D 87 GLU cc_start: 0.7970 (pm20) cc_final: 0.7561 (pm20) REVERT: D 156 MET cc_start: 0.8432 (mpp) cc_final: 0.8199 (mpp) outliers start: 38 outliers final: 25 residues processed: 197 average time/residue: 0.2084 time to fit residues: 59.6331 Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 9 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10916 Z= 0.211 Angle : 0.582 9.604 14764 Z= 0.299 Chirality : 0.041 0.143 1656 Planarity : 0.003 0.032 1814 Dihedral : 4.112 20.038 1448 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.36 % Allowed : 19.14 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1292 helix: 0.85 (0.22), residues: 628 sheet: 0.16 (0.45), residues: 159 loop : -1.57 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.019 0.001 PHE B 175 TYR 0.016 0.001 TYR B 206 ARG 0.006 0.000 ARG B 80 *********************** 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: 39 poor density : 176 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9176 (mm) cc_final: 0.8863 (tp) REVERT: A 252 TYR cc_start: 0.7486 (m-80) cc_final: 0.7267 (m-80) REVERT: A 264 LEU cc_start: 0.8296 (pt) cc_final: 0.7928 (pt) REVERT: A 274 PHE cc_start: 0.7340 (m-10) cc_final: 0.7063 (m-10) REVERT: B 12 GLN cc_start: 0.8801 (pm20) cc_final: 0.8594 (pm20) REVERT: C 20 ARG cc_start: 0.8624 (mtt90) cc_final: 0.8281 (mtt-85) REVERT: C 101 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8116 (mt) REVERT: C 157 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7532 (t-90) REVERT: C 177 GLN cc_start: 0.8301 (tp-100) cc_final: 0.8073 (tp-100) REVERT: C 201 MET cc_start: 0.7819 (mmp) cc_final: 0.7520 (mmm) REVERT: C 236 MET cc_start: 0.7054 (ppp) cc_final: 0.6753 (tmm) REVERT: C 261 GLU cc_start: 0.7069 (pp20) cc_final: 0.6770 (pp20) REVERT: C 267 GLU cc_start: 0.7564 (mp0) cc_final: 0.7238 (mp0) REVERT: C 357 GLN cc_start: 0.8164 (mt0) cc_final: 0.7873 (tm-30) REVERT: C 361 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7488 (t70) REVERT: D 20 ASP cc_start: 0.6618 (p0) cc_final: 0.5952 (t0) REVERT: D 87 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: D 156 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: D 249 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6552 (mm-30) outliers start: 39 outliers final: 27 residues processed: 203 average time/residue: 0.2120 time to fit residues: 62.4663 Evaluate side-chains 191 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 197 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 127 ILE Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 153 SER 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 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 87 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.8980 chunk 13 optimal weight: 0.0060 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10916 Z= 0.160 Angle : 0.578 9.923 14764 Z= 0.292 Chirality : 0.041 0.137 1656 Planarity : 0.003 0.033 1814 Dihedral : 3.951 19.024 1448 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.76 % Allowed : 20.69 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1292 helix: 0.99 (0.22), residues: 624 sheet: 0.19 (0.45), residues: 162 loop : -1.50 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.022 0.001 PHE D 152 TYR 0.015 0.001 TYR B 206 ARG 0.003 0.000 ARG A 392 *********************** 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 216 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8204 (t80) REVERT: A 264 LEU cc_start: 0.8280 (pt) cc_final: 0.7906 (pt) REVERT: A 274 PHE cc_start: 0.7338 (m-10) cc_final: 0.7072 (m-10) REVERT: C 20 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8290 (mtt-85) REVERT: C 101 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 127 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: C 157 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: C 177 GLN cc_start: 0.8287 (tp-100) cc_final: 0.8072 (tp-100) REVERT: C 201 MET cc_start: 0.7810 (mmp) cc_final: 0.7513 (mmm) REVERT: C 261 GLU cc_start: 0.7026 (pp20) cc_final: 0.6710 (pp20) REVERT: C 267 GLU cc_start: 0.7537 (mp0) cc_final: 0.7197 (mp0) REVERT: C 361 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7375 (t70) REVERT: D 12 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: D 87 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: D 156 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8182 (mpp) REVERT: D 249 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6654 (mm-30) outliers start: 32 outliers final: 20 residues processed: 203 average time/residue: 0.2053 time to fit residues: 61.1785 Evaluate side-chains 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 PHE Chi-restraints excluded: chain A residue 197 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 91 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 172 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 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 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 12 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 156 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 0.0010 overall best weight: 1.8050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10916 Z= 0.304 Angle : 0.648 11.948 14764 Z= 0.329 Chirality : 0.043 0.202 1656 Planarity : 0.003 0.033 1814 Dihedral : 4.125 19.010 1448 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.45 % Allowed : 21.47 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1292 helix: 0.85 (0.22), residues: 626 sheet: 0.02 (0.45), residues: 164 loop : -1.49 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 71 HIS 0.005 0.001 HIS C 350 PHE 0.016 0.002 PHE B 195 TYR 0.019 0.001 TYR B 206 ARG 0.002 0.000 ARG D 17 *********************** 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 214 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9179 (mm) cc_final: 0.8861 (tp) REVERT: A 264 LEU cc_start: 0.8251 (pt) cc_final: 0.7875 (pt) REVERT: A 274 PHE cc_start: 0.7397 (m-10) cc_final: 0.7111 (m-10) REVERT: C 20 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8315 (mtt-85) REVERT: C 101 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8005 (mp) REVERT: C 127 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: C 157 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7568 (t-90) REVERT: C 177 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8103 (tp-100) REVERT: C 201 MET cc_start: 0.7985 (mmp) cc_final: 0.7622 (mmm) REVERT: C 261 GLU cc_start: 0.7170 (pp20) cc_final: 0.6852 (pp20) REVERT: C 267 GLU cc_start: 0.7563 (mp0) cc_final: 0.7220 (mp0) REVERT: C 361 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7438 (t70) REVERT: D 100 GLU cc_start: 0.8078 (pm20) cc_final: 0.7853 (pm20) REVERT: D 156 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7986 (mpp) REVERT: D 249 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6804 (mm-30) outliers start: 40 outliers final: 29 residues processed: 204 average time/residue: 0.2087 time to fit residues: 62.1960 Evaluate side-chains 195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 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 118 ILE 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 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 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 87 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 118 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10916 Z= 0.195 Angle : 0.628 12.588 14764 Z= 0.317 Chirality : 0.042 0.198 1656 Planarity : 0.003 0.035 1814 Dihedral : 4.041 17.287 1448 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.59 % Allowed : 21.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1292 helix: 0.91 (0.22), residues: 625 sheet: 0.02 (0.46), residues: 161 loop : -1.50 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 362 HIS 0.004 0.001 HIS C 175 PHE 0.025 0.001 PHE B 175 TYR 0.016 0.001 TYR B 206 ARG 0.004 0.000 ARG C 263 *********************** 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 205 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9148 (mm) cc_final: 0.8800 (tp) REVERT: A 264 LEU cc_start: 0.8222 (pt) cc_final: 0.7848 (pt) REVERT: A 274 PHE cc_start: 0.7368 (m-10) cc_final: 0.7092 (m-10) REVERT: A 350 HIS cc_start: 0.4855 (p-80) cc_final: 0.4502 (p-80) REVERT: C 20 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8316 (mtt-85) REVERT: C 101 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 157 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7539 (t-90) REVERT: C 201 MET cc_start: 0.7961 (mmp) cc_final: 0.7647 (mmm) REVERT: C 261 GLU cc_start: 0.7011 (pp20) cc_final: 0.6647 (pp20) REVERT: C 263 ARG cc_start: 0.7018 (mtm110) cc_final: 0.6419 (mtm-85) REVERT: C 267 GLU cc_start: 0.7560 (mp0) cc_final: 0.7198 (mp0) REVERT: D 100 GLU cc_start: 0.8170 (pm20) cc_final: 0.7915 (pm20) REVERT: D 156 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: D 249 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6693 (mm-30) outliers start: 30 outliers final: 23 residues processed: 195 average time/residue: 0.2164 time to fit residues: 61.1369 Evaluate side-chains 195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 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 118 ILE 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 101 LEU 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 12 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10916 Z= 0.332 Angle : 0.674 11.885 14764 Z= 0.346 Chirality : 0.043 0.217 1656 Planarity : 0.003 0.042 1814 Dihedral : 4.145 17.032 1448 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.59 % Allowed : 21.90 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1292 helix: 0.81 (0.22), residues: 626 sheet: -0.03 (0.45), residues: 164 loop : -1.49 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 71 HIS 0.006 0.001 HIS C 175 PHE 0.030 0.002 PHE C 181 TYR 0.017 0.001 TYR B 206 ARG 0.005 0.000 ARG B 80 ********************** 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: 30 poor density : 169 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ILE cc_start: 0.9204 (mm) cc_final: 0.8883 (tp) REVERT: A 264 LEU cc_start: 0.8239 (pt) cc_final: 0.7891 (pt) REVERT: A 274 PHE cc_start: 0.7404 (m-10) cc_final: 0.7120 (m-10) REVERT: C 20 ARG cc_start: 0.8676 (mtt90) cc_final: 0.8329 (mtt-85) REVERT: C 101 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7909 (mt) REVERT: C 157 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (t-90) REVERT: C 261 GLU cc_start: 0.7141 (pp20) cc_final: 0.6783 (pp20) REVERT: C 263 ARG cc_start: 0.7097 (mtm110) cc_final: 0.6638 (mtm-85) REVERT: C 267 GLU cc_start: 0.7600 (mp0) cc_final: 0.7262 (mp0) REVERT: D 156 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8096 (mpp) REVERT: D 249 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6909 (mm-30) outliers start: 30 outliers final: 27 residues processed: 192 average time/residue: 0.2199 time to fit residues: 60.8034 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 : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 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 118 ILE 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 101 LEU Chi-restraints excluded: chain C residue 107 ASN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.154394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108110 restraints weight = 19919.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111425 restraints weight = 11703.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112520 restraints weight = 8714.807| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 10916 Z= 0.345 Angle : 0.946 59.199 14764 Z= 0.554 Chirality : 0.042 0.216 1656 Planarity : 0.003 0.042 1814 Dihedral : 4.168 17.045 1448 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.76 % Allowed : 21.81 % Favored : 75.43 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1292 helix: 0.78 (0.22), residues: 626 sheet: -0.04 (0.45), residues: 164 loop : -1.49 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 71 HIS 0.005 0.001 HIS C 175 PHE 0.028 0.002 PHE C 181 TYR 0.014 0.001 TYR B 206 ARG 0.002 0.000 ARG A 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.10 seconds wall clock time: 39 minutes 56.87 seconds (2396.87 seconds total)