Starting phenix.real_space_refine on Thu May 15 01:24:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dn8_27556/05_2025/8dn8_27556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dn8_27556/05_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_27556/05_2025/8dn8_27556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dn8_27556/05_2025/8dn8_27556.map" model { file = "/net/cci-nas-00/data/ceres_data/8dn8_27556/05_2025/8dn8_27556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dn8_27556/05_2025/8dn8_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.04, per 1000 atoms: 0.57 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 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: 1.07 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: 2.86 Time building geometry restraints manager: 2.80 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: 0.02 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.950 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- 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 : 9.82 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 Details of bonding type rmsd hydrogen bonds : bond 0.14665 ( 467) hydrogen bonds : angle 5.96116 ( 1377) covalent geometry : bond 0.00426 (10916) covalent geometry : angle 0.61918 (14764) *********************** 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 : 1.227 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: 0.1993 time to fit residues: 67.6458 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 : 1.167 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.156403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.108666 restraints weight = 20046.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.112816 restraints weight = 10548.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115405 restraints weight = 7446.781| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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= 0.218 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 Details of bonding type rmsd hydrogen bonds : bond 0.04829 ( 467) hydrogen bonds : angle 4.89744 ( 1377) covalent geometry : bond 0.00524 (10916) covalent geometry : angle 0.64332 (14764) *********************** 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 : 1.195 Fit side-chains REVERT: A 147 ILE cc_start: 0.9122 (mm) cc_final: 0.8840 (tp) REVERT: A 252 TYR cc_start: 0.7207 (m-80) cc_final: 0.6959 (m-80) REVERT: B 56 THR cc_start: 0.8529 (m) cc_final: 0.8140 (p) REVERT: C 127 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: C 157 HIS cc_start: 0.7905 (m-70) cc_final: 0.7497 (t-90) REVERT: C 177 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7613 (tp-100) REVERT: C 201 MET cc_start: 0.7536 (mmp) cc_final: 0.7315 (mmm) REVERT: C 236 MET cc_start: 0.7013 (ppp) cc_final: 0.6613 (tmm) REVERT: C 261 GLU cc_start: 0.6601 (pp20) cc_final: 0.6392 (pp20) REVERT: D 8 GLU cc_start: 0.8194 (tp30) cc_final: 0.7881 (tp30) REVERT: D 13 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8364 (tm-30) REVERT: D 20 ASP cc_start: 0.6317 (p0) cc_final: 0.5794 (t0) REVERT: D 145 TYR cc_start: 0.8442 (t80) cc_final: 0.8226 (t80) REVERT: D 152 PHE cc_start: 0.8225 (t80) cc_final: 0.7970 (t80) REVERT: D 156 MET cc_start: 0.8277 (mpp) cc_final: 0.7556 (mpp) outliers start: 26 outliers final: 17 residues processed: 201 average time/residue: 0.2033 time to fit residues: 59.4583 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 : 1.156 ------------------------------------------------------------------------------- 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 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** 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 = 0.3906 r_free = 0.3906 target = 0.143319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098719 restraints weight = 20573.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098109 restraints weight = 14170.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098538 restraints weight = 10287.515| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10916 Z= 0.140 Angle : 0.594 14.276 14764 Z= 0.301 Chirality : 0.042 0.135 1656 Planarity : 0.003 0.030 1814 Dihedral : 4.212 23.634 1448 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.50 % Allowed : 13.88 % Favored : 83.62 % 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: -0.27 (0.24), residues: 1292 helix: 0.86 (0.22), residues: 628 sheet: 0.04 (0.44), residues: 155 loop : -1.56 (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 A 350 PHE 0.026 0.001 PHE C 152 TYR 0.018 0.001 TYR B 206 ARG 0.005 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 467) hydrogen bonds : angle 4.64079 ( 1377) covalent geometry : bond 0.00332 (10916) covalent geometry : angle 0.59423 (14764) *********************** 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 217 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 274 PHE cc_start: 0.7537 (m-10) cc_final: 0.7296 (m-10) REVERT: B 56 THR cc_start: 0.8501 (m) cc_final: 0.8113 (p) REVERT: C 20 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8254 (mtt-85) REVERT: C 127 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: C 157 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: C 177 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7685 (tp-100) REVERT: C 201 MET cc_start: 0.7549 (mmp) cc_final: 0.7299 (mmm) REVERT: C 261 GLU cc_start: 0.6703 (pp20) cc_final: 0.6433 (pp20) REVERT: D 8 GLU cc_start: 0.8252 (tp30) cc_final: 0.7946 (tp30) REVERT: D 12 GLN cc_start: 0.8146 (pt0) cc_final: 0.7818 (pt0) REVERT: D 20 ASP cc_start: 0.6600 (p0) cc_final: 0.6058 (t0) REVERT: D 156 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7892 (mpp) outliers start: 29 outliers final: 17 residues processed: 206 average time/residue: 0.2184 time to fit residues: 64.1445 Evaluate side-chains 187 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 10.0000 chunk 67 optimal weight: 0.0870 chunk 78 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.142588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094521 restraints weight = 20307.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096698 restraints weight = 13286.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097957 restraints weight = 10179.863| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10916 Z= 0.155 Angle : 0.592 9.849 14764 Z= 0.303 Chirality : 0.042 0.140 1656 Planarity : 0.003 0.028 1814 Dihedral : 4.200 22.485 1448 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.84 % Allowed : 16.72 % Favored : 80.43 % 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: -0.22 (0.24), residues: 1292 helix: 0.87 (0.22), residues: 628 sheet: 0.20 (0.45), residues: 155 loop : -1.55 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 26 HIS 0.007 0.001 HIS A 350 PHE 0.019 0.001 PHE C 152 TYR 0.017 0.001 TYR A 252 ARG 0.006 0.001 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 467) hydrogen bonds : angle 4.56967 ( 1377) covalent geometry : bond 0.00370 (10916) covalent geometry : angle 0.59243 (14764) *********************** 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 212 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.8329 (mmm) cc_final: 0.8005 (mmm) REVERT: A 350 HIS cc_start: 0.4891 (p-80) cc_final: 0.4588 (p-80) REVERT: C 20 ARG cc_start: 0.8577 (mtt90) cc_final: 0.8267 (mtt-85) REVERT: C 101 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 127 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: C 157 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7524 (t-90) REVERT: C 177 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7848 (tp-100) REVERT: C 201 MET cc_start: 0.7742 (mmp) cc_final: 0.7481 (mmm) REVERT: C 236 MET cc_start: 0.7261 (ppp) cc_final: 0.7011 (tmm) REVERT: C 261 GLU cc_start: 0.6951 (pp20) cc_final: 0.6663 (pp20) REVERT: D 20 ASP cc_start: 0.6579 (p0) cc_final: 0.5916 (t0) REVERT: D 156 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7849 (mpp) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 0.2040 time to fit residues: 59.8861 Evaluate side-chains 188 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110043 restraints weight = 20145.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109998 restraints weight = 11842.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111971 restraints weight = 8563.323| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2497 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= 0.234 Angle : 0.637 7.760 14764 Z= 0.329 Chirality : 0.044 0.133 1656 Planarity : 0.003 0.031 1814 Dihedral : 4.305 18.589 1448 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.88 % Allowed : 18.45 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.24), residues: 1292 helix: 0.71 (0.21), residues: 628 sheet: 0.14 (0.42), residues: 170 loop : -1.63 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 26 HIS 0.004 0.001 HIS B 212 PHE 0.018 0.002 PHE D 175 TYR 0.032 0.002 TYR C 142 ARG 0.005 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 467) hydrogen bonds : angle 4.66148 ( 1377) covalent geometry : bond 0.00562 (10916) covalent geometry : angle 0.63687 (14764) *********************** 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 214 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8086 (pt) cc_final: 0.7789 (pt) REVERT: A 274 PHE cc_start: 0.7530 (m-10) cc_final: 0.7251 (m-10) REVERT: A 350 HIS cc_start: 0.5353 (p-80) cc_final: 0.4932 (p-80) REVERT: C 20 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8321 (mtt-85) REVERT: C 101 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8387 (mt) REVERT: C 127 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: C 157 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7529 (t-90) REVERT: C 177 GLN cc_start: 0.8216 (tp-100) cc_final: 0.8004 (tp-100) REVERT: C 201 MET cc_start: 0.7665 (mmp) cc_final: 0.7426 (mmm) REVERT: C 236 MET cc_start: 0.7040 (ppp) cc_final: 0.6636 (tmm) REVERT: C 261 GLU cc_start: 0.7112 (pp20) cc_final: 0.6841 (pp20) REVERT: C 361 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7248 (t70) REVERT: D 20 ASP cc_start: 0.6719 (p0) cc_final: 0.6076 (t0) REVERT: D 87 GLU cc_start: 0.7811 (pm20) cc_final: 0.7417 (pm20) REVERT: D 156 MET cc_start: 0.8396 (mpp) cc_final: 0.7986 (mpp) REVERT: D 249 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7163 (mm-30) outliers start: 45 outliers final: 31 residues processed: 201 average time/residue: 0.2095 time to fit residues: 60.6799 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 : 1.348 ------------------------------------------------------------------------------- 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 56 THR 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 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 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 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 11 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** 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 = 0.4168 r_free = 0.4168 target = 0.156657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114271 restraints weight = 20223.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114659 restraints weight = 12555.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115683 restraints weight = 8312.049| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10916 Z= 0.119 Angle : 0.582 8.615 14764 Z= 0.299 Chirality : 0.041 0.150 1656 Planarity : 0.003 0.034 1814 Dihedral : 4.141 20.373 1448 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.28 % Allowed : 19.57 % Favored : 77.16 % 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: -0.21 (0.24), residues: 1292 helix: 0.89 (0.22), residues: 626 sheet: 0.10 (0.45), residues: 157 loop : -1.50 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.016 0.001 PHE C 255 TYR 0.018 0.001 TYR B 206 ARG 0.006 0.000 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 467) hydrogen bonds : angle 4.42764 ( 1377) covalent geometry : bond 0.00276 (10916) covalent geometry : angle 0.58236 (14764) *********************** 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 220 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8409 (mmm) REVERT: A 147 ILE cc_start: 0.9198 (mm) cc_final: 0.8856 (tp) REVERT: A 264 LEU cc_start: 0.8035 (pt) cc_final: 0.7749 (pt) REVERT: A 274 PHE cc_start: 0.7604 (m-10) cc_final: 0.7332 (m-10) REVERT: A 334 MET cc_start: 0.8165 (mmm) cc_final: 0.7868 (mmm) REVERT: A 350 HIS cc_start: 0.5166 (p-80) cc_final: 0.4836 (p-80) REVERT: A 393 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6922 (tptp) REVERT: C 20 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8312 (mtt-85) REVERT: C 101 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8264 (mt) REVERT: C 157 HIS cc_start: 0.7607 (OUTLIER) cc_final: 0.7295 (t-90) REVERT: C 201 MET cc_start: 0.7478 (mmp) cc_final: 0.7231 (mmm) REVERT: C 236 MET cc_start: 0.7020 (ppp) cc_final: 0.6673 (tmm) REVERT: C 261 GLU cc_start: 0.6826 (pp20) cc_final: 0.6594 (pp20) REVERT: C 267 GLU cc_start: 0.7689 (mp0) cc_final: 0.7405 (mp0) REVERT: C 357 GLN cc_start: 0.7868 (mt0) cc_final: 0.7550 (tm-30) REVERT: D 8 GLU cc_start: 0.8313 (tp30) cc_final: 0.7876 (tp30) REVERT: D 12 GLN cc_start: 0.8294 (pt0) cc_final: 0.7941 (pt0) REVERT: D 20 ASP cc_start: 0.6611 (p0) cc_final: 0.5932 (t0) REVERT: D 249 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6999 (mm-30) outliers start: 38 outliers final: 22 residues processed: 206 average time/residue: 0.2234 time to fit residues: 66.4096 Evaluate side-chains 193 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 393 LYS 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 0.0050 chunk 7 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.110938 restraints weight = 20361.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.115242 restraints weight = 10472.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.118006 restraints weight = 7223.731| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10916 Z= 0.111 Angle : 0.585 10.586 14764 Z= 0.299 Chirality : 0.041 0.135 1656 Planarity : 0.003 0.039 1814 Dihedral : 4.013 19.068 1448 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.10 % Allowed : 20.78 % Favored : 76.12 % 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: -0.19 (0.24), residues: 1292 helix: 0.88 (0.22), residues: 625 sheet: 0.12 (0.45), residues: 158 loop : -1.46 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 26 HIS 0.005 0.001 HIS C 175 PHE 0.023 0.001 PHE D 152 TYR 0.018 0.001 TYR B 206 ARG 0.003 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 467) hydrogen bonds : angle 4.38658 ( 1377) covalent geometry : bond 0.00251 (10916) covalent geometry : angle 0.58528 (14764) *********************** 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 219 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 264 LEU cc_start: 0.8075 (pt) cc_final: 0.7770 (pt) REVERT: A 274 PHE cc_start: 0.7570 (m-10) cc_final: 0.7262 (m-10) REVERT: A 334 MET cc_start: 0.8203 (mmm) cc_final: 0.7940 (mmm) REVERT: A 350 HIS cc_start: 0.5428 (p-80) cc_final: 0.4969 (p-80) REVERT: C 20 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8326 (mtt-85) REVERT: C 101 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 157 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7394 (t-90) REVERT: C 177 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7848 (tp-100) REVERT: C 201 MET cc_start: 0.7651 (mmp) cc_final: 0.7342 (mmm) REVERT: C 236 MET cc_start: 0.7262 (ppp) cc_final: 0.6982 (tmm) REVERT: C 261 GLU cc_start: 0.6830 (pp20) cc_final: 0.6581 (pp20) REVERT: C 267 GLU cc_start: 0.7684 (mp0) cc_final: 0.7427 (mp0) REVERT: C 357 GLN cc_start: 0.7774 (mt0) cc_final: 0.7510 (tm-30) REVERT: D 8 GLU cc_start: 0.8317 (tp30) cc_final: 0.7881 (tp30) REVERT: D 12 GLN cc_start: 0.8255 (pt0) cc_final: 0.7922 (pt0) REVERT: D 249 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6912 (mm-30) outliers start: 36 outliers final: 23 residues processed: 206 average time/residue: 0.2326 time to fit residues: 70.2015 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 : 1.261 ------------------------------------------------------------------------------- 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 12 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 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 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 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 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 28 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.157726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115553 restraints weight = 19955.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116269 restraints weight = 11112.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116417 restraints weight = 8726.363| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2824 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= 0.117 Angle : 0.596 10.835 14764 Z= 0.300 Chirality : 0.041 0.135 1656 Planarity : 0.003 0.038 1814 Dihedral : 3.939 18.970 1448 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.84 % Allowed : 21.64 % 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: -0.19 (0.24), residues: 1292 helix: 0.89 (0.22), residues: 625 sheet: 0.06 (0.45), residues: 164 loop : -1.48 (0.26), residues: 503 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 0.023 0.001 PHE D 152 TYR 0.014 0.001 TYR B 206 ARG 0.002 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 467) hydrogen bonds : angle 4.32230 ( 1377) covalent geometry : bond 0.00273 (10916) covalent geometry : angle 0.59648 (14764) *********************** 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 208 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8169 (pt) cc_final: 0.7843 (pt) REVERT: A 274 PHE cc_start: 0.7475 (m-10) cc_final: 0.7204 (m-10) REVERT: A 334 MET cc_start: 0.8324 (mmm) cc_final: 0.8095 (mmm) REVERT: A 350 HIS cc_start: 0.5511 (p-80) cc_final: 0.5032 (p-80) REVERT: A 393 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6554 (tptp) REVERT: C 20 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8237 (mtt-85) REVERT: C 101 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 157 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: C 177 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7966 (tp-100) REVERT: C 201 MET cc_start: 0.7826 (mmp) cc_final: 0.7489 (mmm) REVERT: C 261 GLU cc_start: 0.7004 (pp20) cc_final: 0.6704 (pp20) REVERT: C 267 GLU cc_start: 0.7705 (mp0) cc_final: 0.7391 (mp0) REVERT: C 357 GLN cc_start: 0.7914 (mt0) cc_final: 0.7700 (tm-30) REVERT: D 8 GLU cc_start: 0.8474 (tp30) cc_final: 0.8101 (tp30) REVERT: D 12 GLN cc_start: 0.8364 (pt0) cc_final: 0.8077 (pt0) REVERT: D 100 GLU cc_start: 0.8018 (pm20) cc_final: 0.7792 (pm20) REVERT: D 205 MET cc_start: 0.8505 (tpt) cc_final: 0.8257 (tpt) outliers start: 33 outliers final: 26 residues processed: 198 average time/residue: 0.2187 time to fit residues: 62.6179 Evaluate side-chains 194 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 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 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 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.157398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109724 restraints weight = 20218.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113819 restraints weight = 10601.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116535 restraints weight = 7432.228| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10916 Z= 0.134 Angle : 0.616 11.567 14764 Z= 0.310 Chirality : 0.041 0.169 1656 Planarity : 0.003 0.054 1814 Dihedral : 3.926 17.472 1448 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.93 % Allowed : 21.64 % 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: -0.18 (0.24), residues: 1292 helix: 0.87 (0.22), residues: 625 sheet: 0.12 (0.45), residues: 162 loop : -1.45 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 71 HIS 0.004 0.001 HIS C 175 PHE 0.022 0.001 PHE D 175 TYR 0.013 0.001 TYR B 206 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 467) hydrogen bonds : angle 4.34533 ( 1377) covalent geometry : bond 0.00319 (10916) covalent geometry : angle 0.61559 (14764) *********************** 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 207 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8089 (pt) cc_final: 0.7787 (pt) REVERT: A 274 PHE cc_start: 0.7576 (m-10) cc_final: 0.7339 (m-10) REVERT: A 334 MET cc_start: 0.8250 (mmm) cc_final: 0.8032 (mmm) REVERT: A 350 HIS cc_start: 0.5316 (p-80) cc_final: 0.4932 (p-80) REVERT: A 393 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6147 (tptp) REVERT: C 20 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8293 (mtt-85) REVERT: C 101 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7968 (mp) REVERT: C 127 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: C 157 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7417 (t-90) REVERT: C 177 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7919 (tp-100) REVERT: C 201 MET cc_start: 0.7737 (mmp) cc_final: 0.7429 (mmm) REVERT: C 261 GLU cc_start: 0.6769 (pp20) cc_final: 0.6524 (pp20) REVERT: C 267 GLU cc_start: 0.7662 (mp0) cc_final: 0.7341 (mp0) REVERT: D 8 GLU cc_start: 0.8366 (tp30) cc_final: 0.8041 (tp30) REVERT: D 12 GLN cc_start: 0.8294 (pt0) cc_final: 0.8002 (pt0) REVERT: D 100 GLU cc_start: 0.8038 (pm20) cc_final: 0.7761 (pm20) REVERT: D 205 MET cc_start: 0.8553 (tpt) cc_final: 0.8250 (tpt) REVERT: D 249 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6686 (mm-30) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.2057 time to fit residues: 59.3203 Evaluate side-chains 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 12 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 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 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 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 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 172 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 0.0270 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.158182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113518 restraints weight = 20082.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115788 restraints weight = 10952.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116019 restraints weight = 7900.339| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2988 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= 0.124 Angle : 0.632 10.773 14764 Z= 0.317 Chirality : 0.041 0.168 1656 Planarity : 0.003 0.048 1814 Dihedral : 3.923 17.573 1448 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.84 % Allowed : 21.55 % Favored : 75.60 % 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: -0.17 (0.24), residues: 1292 helix: 0.90 (0.22), residues: 625 sheet: 0.03 (0.45), residues: 166 loop : -1.44 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 71 HIS 0.006 0.001 HIS C 350 PHE 0.041 0.001 PHE D 152 TYR 0.012 0.001 TYR B 206 ARG 0.003 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 467) hydrogen bonds : angle 4.32429 ( 1377) covalent geometry : bond 0.00289 (10916) covalent geometry : angle 0.63166 (14764) ********************** 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 207 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 152 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 264 LEU cc_start: 0.8199 (pt) cc_final: 0.7868 (pt) REVERT: A 274 PHE cc_start: 0.7447 (m-10) cc_final: 0.7216 (m-10) REVERT: A 334 MET cc_start: 0.8355 (mmm) cc_final: 0.8142 (mmm) REVERT: A 350 HIS cc_start: 0.5391 (p-80) cc_final: 0.4922 (p-80) REVERT: C 20 ARG cc_start: 0.8613 (mtt90) cc_final: 0.8245 (mtt-85) REVERT: C 101 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7944 (mp) REVERT: C 127 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: C 157 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7479 (t-90) REVERT: C 177 GLN cc_start: 0.8279 (tp-100) cc_final: 0.8035 (tp-100) REVERT: C 201 MET cc_start: 0.7946 (mmp) cc_final: 0.7694 (mmm) REVERT: C 261 GLU cc_start: 0.7091 (pp20) cc_final: 0.6781 (pp20) REVERT: C 267 GLU cc_start: 0.7671 (mp0) cc_final: 0.7279 (mp0) REVERT: C 353 MET cc_start: 0.8403 (tpt) cc_final: 0.8180 (tpp) REVERT: D 8 GLU cc_start: 0.8502 (tp30) cc_final: 0.8139 (tp30) REVERT: D 12 GLN cc_start: 0.8375 (pt0) cc_final: 0.8069 (pt0) REVERT: D 100 GLU cc_start: 0.8138 (pm20) cc_final: 0.7855 (pm20) REVERT: D 205 MET cc_start: 0.8465 (tpt) cc_final: 0.8197 (tpt) REVERT: D 249 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6842 (mm-30) outliers start: 33 outliers final: 27 residues processed: 198 average time/residue: 0.2022 time to fit residues: 58.7226 Evaluate side-chains 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 12 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 127 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 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 327 LYS 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 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 172 ILE 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 73 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS B 113 ASN ** C 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN C 361 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.156751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113150 restraints weight = 20122.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.114263 restraints weight = 11167.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.114861 restraints weight = 8263.307| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10916 Z= 0.140 Angle : 0.633 10.601 14764 Z= 0.320 Chirality : 0.041 0.158 1656 Planarity : 0.003 0.048 1814 Dihedral : 3.924 16.845 1448 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.93 % Allowed : 21.72 % Favored : 75.34 % 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: -0.16 (0.24), residues: 1292 helix: 0.88 (0.22), residues: 625 sheet: 0.12 (0.45), residues: 164 loop : -1.43 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 26 HIS 0.004 0.001 HIS C 175 PHE 0.041 0.001 PHE B 245 TYR 0.013 0.001 TYR B 206 ARG 0.003 0.000 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 467) hydrogen bonds : angle 4.36256 ( 1377) covalent geometry : bond 0.00334 (10916) covalent geometry : angle 0.63269 (14764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.28 seconds wall clock time: 63 minutes 50.14 seconds (3830.14 seconds total)