Starting phenix.real_space_refine on Wed Jul 1 22:34:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u13_26276/07_2026/7u13_26276.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2202 2.51 5 N 531 2.21 5 O 702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "B" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "C" Number of atoms: 1096 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} Conformer: "B" Number of residues, atoms: 135, 1087 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 132} bond proxies already assigned to first conformer: 1094 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.00, per 1000 atoms: 0.29 Number of scatterers: 3456 At special positions: 0 Unit cell: (97.734, 117.066, 31.146, 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 21 16.00 O 702 8.00 N 531 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 183 " " NAG A 302 " - " ASN A 151 " " NAG A 303 " - " ASN A 145 " " NAG A 304 " - " ASN A 164 " " NAG B 301 " - " ASN B 183 " " NAG B 302 " - " ASN B 151 " " NAG B 303 " - " ASN B 145 " " NAG B 304 " - " ASN B 164 " " NAG C 301 " - " ASN C 183 " " NAG C 302 " - " ASN C 151 " " NAG C 303 " - " ASN C 145 " " NAG C 304 " - " ASN C 164 " Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 139.7 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 68.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.322A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 removed outlier: 6.322A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 131 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 177 removed outlier: 9.050A pdb=" N THR A 141 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU B 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR A 143 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE B 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A 145 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASN B 148 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR A 147 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU B 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 149 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE B 152 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASN A 151 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN B 154 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 153 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 156 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 155 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR B 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N ASN B 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N GLU A 163 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N THR B 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER B 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE A 171 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N THR B 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 173 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE B 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 175 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N THR B 141 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N LEU C 144 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYR B 143 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ILE C 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 145 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN C 148 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 147 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU C 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR B 149 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 152 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN B 151 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASN C 154 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR B 153 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN C 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR C 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR B 157 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL C 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLU B 161 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ASN C 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N GLU B 163 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N THR C 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 165 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLN C 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 167 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLN C 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL B 169 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER C 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 171 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N THR C 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS B 173 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE C 176 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 175 " --> pdb=" O ILE C 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.630A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.458A pdb=" N THR A 185 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.929A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 196 " --> pdb=" O TYR C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.278A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219 removed outlier: 6.960A pdb=" N MET A 210 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 228 removed outlier: 6.853A pdb=" N ASN B 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN C 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.470A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 249 through 253 removed outlier: 6.871A pdb=" N TYR B 250 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR C 250 " --> pdb=" O GLN B 249 " (cutoff:3.500A) 53 hydrogen bonds defined for protein. 156 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: 0.28 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 9 1.21 - 1.36: 1059 1.36 - 1.51: 1090 1.51 - 1.66: 1322 1.66 - 1.81: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" CG PRO C 189 " pdb=" CD PRO C 189 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.43e+01 bond pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.40e+01 bond pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 1.503 1.174 0.329 3.40e-02 8.65e+02 9.35e+01 bond pdb=" CB PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 1.492 1.063 0.429 5.00e-02 4.00e+02 7.38e+01 bond pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 1.492 1.063 0.429 5.00e-02 4.00e+02 7.38e+01 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 4779 14.77 - 29.54: 3 29.54 - 44.31: 3 44.31 - 59.08: 0 59.08 - 73.86: 3 Bond angle restraints: 4788 Sorted by residual: angle pdb=" CB PRO A 189 " pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 106.10 179.96 -73.86 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 106.10 179.92 -73.82 3.20e+00 9.77e-02 5.32e+02 angle pdb=" CB PRO C 189 " pdb=" CG PRO C 189 " pdb=" CD PRO C 189 " ideal model delta sigma weight residual 106.10 179.89 -73.79 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO A 189 " pdb=" CD PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 103.20 73.84 29.36 1.50e+00 4.44e-01 3.83e+02 angle pdb=" N PRO C 189 " pdb=" CD PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 103.20 73.95 29.25 1.50e+00 4.44e-01 3.80e+02 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 1879 26.07 - 52.13: 126 52.13 - 78.20: 9 78.20 - 104.27: 4 104.27 - 130.33: 1 Dihedral angle restraints: 2019 sinusoidal: 786 harmonic: 1233 Sorted by residual: dihedral pdb=" N PRO A 189 " pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " pdb=" CB PRO A 189 " ideal model delta sinusoidal sigma weight residual -30.00 -160.33 130.33 1 1.50e+01 4.44e-03 7.03e+01 dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 33.46 59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " pdb=" CB CYS B 253 " ideal model delta sinusoidal sigma weight residual 93.00 33.48 59.52 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 438 0.072 - 0.143: 139 0.143 - 0.215: 26 0.215 - 0.286: 0 0.286 - 0.358: 3 Chirality restraints: 606 Sorted by residual: chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.008 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR A 157 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 157 " 0.009 2.00e-02 2.50e+03 1.43e-02 4.11e+00 pdb=" CG TYR B 157 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 157 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 157 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 157 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 157 " 0.009 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR C 157 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 157 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 157 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 157 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 157 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 157 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 157 " -0.000 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 82 2.68 - 3.23: 3267 3.23 - 3.79: 5409 3.79 - 4.34: 6959 4.34 - 4.90: 12721 Nonbonded interactions: 28438 Sorted by model distance: nonbonded pdb=" OH TYR A 197 " pdb=" NZ LYS B 220 " model vdw 2.120 3.120 nonbonded pdb=" NE2 GLN C 229 " pdb=" OG1 THR C 234 " model vdw 2.139 3.120 nonbonded pdb=" NE2 GLN B 229 " pdb=" OG1 THR B 234 " model vdw 2.139 3.120 nonbonded pdb=" NE2 GLN A 229 " pdb=" OG1 THR A 234 " model vdw 2.140 3.120 nonbonded pdb=" OH TYR B 197 " pdb=" NZ LYS C 220 " model vdw 2.168 3.120 ... (remaining 28433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.410 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4741 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 : 0.018 0.429 3531 Z= 0.536 Angle : 2.429 73.856 4830 Z= 1.081 Chirality : 0.071 0.358 606 Planarity : 0.006 0.049 579 Dihedral : 16.463 130.333 1224 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 29.95 Ramachandran Plot: Outliers : 0.75 % Allowed : 11.28 % Favored : 87.97 % Rotamer: Outliers : 6.30 % Allowed : 3.15 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 247 TYR 0.033 0.005 TYR A 157 PHE 0.016 0.004 PHE A 171 HIS 0.003 0.002 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.01758 / 0.54 ( 3516) covalent geometry : angle 2.43083 / 1.08 ( 4788) SS BOND : bond 0.00382 / 0.19 ( 3) SS BOND : angle 3.45170 / 1.86 ( 6) hydrogen bonds : bond 0.12713 / 8.94 ( 53) hydrogen bonds : angle 8.17157 / 5.56 ( 156) link_NAG-ASN : bond 0.00487 / 0.30 ( 12) link_NAG-ASN : angle 1.98188 / 1.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4399 (mmm) cc_final: 0.3481 (ptt) REVERT: B 231 THR cc_start: 0.6681 (p) cc_final: 0.6419 (p) REVERT: C 219 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5797 (mm) outliers start: 24 outliers final: 9 residues processed: 136 average time/residue: 0.3501 time to fit residues: 49.2401 Evaluate side-chains 75 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 219 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 170 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5672 r_free = 0.5672 target = 0.323064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5965 r_free = 0.5965 target = 0.284943 restraints weight = 29130.294| |-----------------------------------------------------------------------------| r_work (start): 0.5562 rms_B_bonded: 5.48 r_work: 0.5912 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.5912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5554 r_free = 0.5554 target_work(ls_wunit_k1) = 0.306 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5552 r_free = 0.5552 target_work(ls_wunit_k1) = 0.306 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.5552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 3531 Z= 0.292 Angle : 1.078 9.491 4830 Z= 0.562 Chirality : 0.065 0.316 606 Planarity : 0.006 0.059 579 Dihedral : 10.430 57.977 477 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 8.14 % Allowed : 18.37 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.022 0.004 TYR C 248 PHE 0.013 0.003 PHE B 171 HIS 0.009 0.004 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 ( 3516) covalent geometry : angle 1.04734 / 0.56 ( 4788) SS BOND : bond 0.01223 / 0.62 ( 3) SS BOND : angle 3.21532 / 1.73 ( 6) hydrogen bonds : bond 0.05030 / 3.11 ( 53) hydrogen bonds : angle 6.92071 / 4.96 ( 156) link_NAG-ASN : bond 0.00633 / 0.41 ( 12) link_NAG-ASN : angle 2.89177 / 1.80 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4776 (mmm) cc_final: 0.2139 (ptt) REVERT: A 245 GLN cc_start: 0.6835 (mp10) cc_final: 0.6278 (tt0) REVERT: B 242 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6613 (mt0) REVERT: C 216 LEU cc_start: 0.7877 (mm) cc_final: 0.7222 (tt) REVERT: C 250 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.4998 (p90) outliers start: 31 outliers final: 7 residues processed: 101 average time/residue: 0.3174 time to fit residues: 33.3049 Evaluate side-chains 78 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5660 r_free = 0.5660 target = 0.317831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5966 r_free = 0.5966 target = 0.279713 restraints weight = 33762.380| |-----------------------------------------------------------------------------| r_work (start): 0.5551 rms_B_bonded: 5.19 r_work: 0.5904 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.5904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5542 r_free = 0.5542 target_work(ls_wunit_k1) = 0.301 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5542 r_free = 0.5542 target_work(ls_wunit_k1) = 0.301 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.5542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.8887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 3531 Z= 0.264 Angle : 1.045 11.890 4830 Z= 0.544 Chirality : 0.062 0.284 606 Planarity : 0.005 0.038 579 Dihedral : 7.313 22.899 459 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 6.30 % Allowed : 28.08 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 180 TYR 0.020 0.003 TYR C 236 PHE 0.015 0.003 PHE B 171 HIS 0.009 0.003 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 ( 3516) covalent geometry : angle 1.01885 / 0.54 ( 4788) SS BOND : bond 0.01170 / 0.59 ( 3) SS BOND : angle 2.87000 / 1.56 ( 6) hydrogen bonds : bond 0.05215 / 2.97 ( 53) hydrogen bonds : angle 6.76202 / 4.70 ( 156) link_NAG-ASN : bond 0.00652 / 0.39 ( 12) link_NAG-ASN : angle 2.66896 / 1.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 207 MET cc_start: 0.1259 (tpt) cc_final: 0.0990 (tmt) REVERT: A 210 MET cc_start: 0.5253 (mmm) cc_final: 0.2706 (ptt) outliers start: 24 outliers final: 12 residues processed: 94 average time/residue: 0.2992 time to fit residues: 29.3265 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN C 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5634 r_free = 0.5634 target = 0.313029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5963 r_free = 0.5963 target = 0.276429 restraints weight = 19299.219| |-----------------------------------------------------------------------------| r_work (start): 0.5545 rms_B_bonded: 3.68 r_work: 0.5912 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.5870 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.5870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5498 r_free = 0.5498 target_work(ls_wunit_k1) = 0.294 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5498 r_free = 0.5498 target_work(ls_wunit_k1) = 0.294 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.5498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 1.0049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 3531 Z= 0.264 Angle : 1.046 10.816 4830 Z= 0.538 Chirality : 0.064 0.306 606 Planarity : 0.004 0.030 579 Dihedral : 7.300 23.614 459 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 8.66 % Allowed : 26.51 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.021 0.003 TYR C 125 PHE 0.018 0.003 PHE A 237 HIS 0.007 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 ( 3516) covalent geometry : angle 1.00753 / 0.53 ( 4788) SS BOND : bond 0.01273 / 0.65 ( 3) SS BOND : angle 2.48843 / 1.37 ( 6) hydrogen bonds : bond 0.05477 / 3.39 ( 53) hydrogen bonds : angle 7.15496 / 5.14 ( 156) link_NAG-ASN : bond 0.00588 / 0.36 ( 12) link_NAG-ASN : angle 3.28903 / 2.19 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 184 ILE cc_start: 0.4017 (OUTLIER) cc_final: 0.3540 (pp) REVERT: A 219 ILE cc_start: 0.4332 (OUTLIER) cc_final: 0.3490 (pp) REVERT: B 163 GLU cc_start: 0.5584 (mp0) cc_final: 0.5028 (mp0) REVERT: B 249 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6350 (tt0) outliers start: 33 outliers final: 13 residues processed: 91 average time/residue: 0.2876 time to fit residues: 27.3001 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.309994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5991 r_free = 0.5991 target = 0.275014 restraints weight = 33621.419| |-----------------------------------------------------------------------------| r_work (start): 0.5520 rms_B_bonded: 4.86 r_work: 0.5880 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.5825 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.5825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5457 r_free = 0.5457 target_work(ls_wunit_k1) = 0.290 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5457 r_free = 0.5457 target_work(ls_wunit_k1) = 0.290 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.5457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 1.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3531 Z= 0.227 Angle : 1.000 10.134 4830 Z= 0.514 Chirality : 0.062 0.281 606 Planarity : 0.004 0.026 579 Dihedral : 7.020 22.897 459 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 7.61 % Allowed : 28.35 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 247 TYR 0.018 0.003 TYR C 125 PHE 0.014 0.002 PHE C 171 HIS 0.007 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 ( 3516) covalent geometry : angle 0.96438 / 0.51 ( 4788) SS BOND : bond 0.00806 / 0.40 ( 3) SS BOND : angle 1.14819 / 0.66 ( 6) hydrogen bonds : bond 0.05510 / 3.31 ( 53) hydrogen bonds : angle 6.85089 / 4.92 ( 156) link_NAG-ASN : bond 0.00557 / 0.34 ( 12) link_NAG-ASN : angle 3.20065 / 2.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.080 Fit side-chains REVERT: A 136 ASP cc_start: 0.6321 (t0) cc_final: 0.6110 (t0) REVERT: A 184 ILE cc_start: 0.4050 (OUTLIER) cc_final: 0.3507 (pp) REVERT: A 192 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3623 (pp-130) REVERT: A 219 ILE cc_start: 0.4329 (OUTLIER) cc_final: 0.3507 (pp) REVERT: B 249 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6391 (tt0) REVERT: C 242 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6157 (mt0) outliers start: 29 outliers final: 13 residues processed: 88 average time/residue: 0.3443 time to fit residues: 31.4538 Evaluate side-chains 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 245 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 = 0.5672 r_free = 0.5672 target = 0.320907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5993 r_free = 0.5993 target = 0.283634 restraints weight = 24055.105| |-----------------------------------------------------------------------------| r_work (start): 0.5574 rms_B_bonded: 4.29 r_work: 0.5947 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.5908 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.5908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5526 r_free = 0.5526 target_work(ls_wunit_k1) = 0.301 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5526 r_free = 0.5526 target_work(ls_wunit_k1) = 0.301 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.5526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 1.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3531 Z= 0.160 Angle : 0.896 12.099 4830 Z= 0.463 Chirality : 0.059 0.254 606 Planarity : 0.003 0.018 579 Dihedral : 6.241 19.683 459 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 6.82 % Allowed : 30.45 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 180 TYR 0.014 0.001 TYR A 125 PHE 0.020 0.002 PHE A 237 HIS 0.008 0.003 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 3516) covalent geometry : angle 0.87243 / 0.46 ( 4788) SS BOND : bond 0.00657 / 0.32 ( 3) SS BOND : angle 1.25425 / 0.67 ( 6) hydrogen bonds : bond 0.04341 / 2.89 ( 53) hydrogen bonds : angle 6.75009 / 4.83 ( 156) link_NAG-ASN : bond 0.00479 / 0.31 ( 12) link_NAG-ASN : angle 2.49039 / 1.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.123 Fit side-chains REVERT: A 184 ILE cc_start: 0.4164 (OUTLIER) cc_final: 0.3663 (pp) REVERT: A 219 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3945 (pt) REVERT: A 245 GLN cc_start: 0.6523 (mp10) cc_final: 0.6043 (tt0) REVERT: C 250 TYR cc_start: 0.5795 (OUTLIER) cc_final: 0.5204 (p90) outliers start: 26 outliers final: 10 residues processed: 94 average time/residue: 0.3517 time to fit residues: 34.3010 Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 0.0670 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN B 138 GLN C 148 ASN C 242 GLN C 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.307856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5969 r_free = 0.5969 target = 0.273137 restraints weight = 37708.128| |-----------------------------------------------------------------------------| r_work (start): 0.5511 rms_B_bonded: 5.32 r_work: 0.5869 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.5869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5489 r_free = 0.5489 target_work(ls_wunit_k1) = 0.292 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5488 r_free = 0.5488 target_work(ls_wunit_k1) = 0.292 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.5488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 1.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3531 Z= 0.242 Angle : 1.031 10.714 4830 Z= 0.530 Chirality : 0.064 0.291 606 Planarity : 0.004 0.019 579 Dihedral : 7.075 24.940 459 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 8.14 % Allowed : 28.61 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.020 0.003 TYR C 125 PHE 0.027 0.004 PHE C 237 HIS 0.005 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 ( 3516) covalent geometry : angle 0.99764 / 0.52 ( 4788) SS BOND : bond 0.00986 / 0.48 ( 3) SS BOND : angle 1.54010 / 0.90 ( 6) hydrogen bonds : bond 0.05435 / 3.31 ( 53) hydrogen bonds : angle 6.67369 / 4.77 ( 156) link_NAG-ASN : bond 0.00533 / 0.32 ( 12) link_NAG-ASN : angle 3.15133 / 1.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.135 Fit side-chains REVERT: A 184 ILE cc_start: 0.3994 (OUTLIER) cc_final: 0.3437 (pp) REVERT: A 207 MET cc_start: 0.1719 (tpt) cc_final: 0.1296 (tmt) REVERT: A 219 ILE cc_start: 0.4271 (OUTLIER) cc_final: 0.4031 (pt) REVERT: A 236 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.3539 (t80) outliers start: 31 outliers final: 16 residues processed: 87 average time/residue: 0.3295 time to fit residues: 29.8560 Evaluate side-chains 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 GLN C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.313781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.6000 r_free = 0.6000 target = 0.279495 restraints weight = 28446.341| |-----------------------------------------------------------------------------| r_work (start): 0.5545 rms_B_bonded: 4.64 r_work: 0.5912 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.5866 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.5866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5487 r_free = 0.5487 target_work(ls_wunit_k1) = 0.294 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5488 r_free = 0.5488 target_work(ls_wunit_k1) = 0.294 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.5488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5687 moved from start: 1.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3531 Z= 0.177 Angle : 0.964 12.762 4830 Z= 0.493 Chirality : 0.061 0.257 606 Planarity : 0.003 0.018 579 Dihedral : 6.552 23.347 459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.51 % Allowed : 31.76 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.013 0.002 TYR A 125 PHE 0.021 0.003 PHE A 237 HIS 0.008 0.003 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 3516) covalent geometry : angle 0.94177 / 0.49 ( 4788) SS BOND : bond 0.00724 / 0.36 ( 3) SS BOND : angle 0.81092 / 0.46 ( 6) hydrogen bonds : bond 0.04696 / 3.06 ( 53) hydrogen bonds : angle 6.74705 / 4.84 ( 156) link_NAG-ASN : bond 0.00455 / 0.29 ( 12) link_NAG-ASN : angle 2.56383 / 1.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.119 Fit side-chains REVERT: A 184 ILE cc_start: 0.4024 (OUTLIER) cc_final: 0.3497 (pp) REVERT: A 219 ILE cc_start: 0.4427 (OUTLIER) cc_final: 0.4176 (pt) REVERT: A 236 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.3548 (t80) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.3333 time to fit residues: 28.7775 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5632 r_free = 0.5632 target = 0.313101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.6011 r_free = 0.6011 target = 0.277937 restraints weight = 20786.034| |-----------------------------------------------------------------------------| r_work (start): 0.5545 rms_B_bonded: 4.01 r_work: 0.5908 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.5864 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.5864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5484 r_free = 0.5484 target_work(ls_wunit_k1) = 0.292 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5483 r_free = 0.5483 target_work(ls_wunit_k1) = 0.292 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.5483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 1.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3531 Z= 0.202 Angle : 1.010 12.023 4830 Z= 0.514 Chirality : 0.062 0.265 606 Planarity : 0.004 0.026 579 Dihedral : 6.675 23.811 459 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 5.77 % Allowed : 33.33 % Favored : 60.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.017 0.002 TYR C 125 PHE 0.022 0.003 PHE A 237 HIS 0.006 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 3516) covalent geometry : angle 0.98598 / 0.51 ( 4788) SS BOND : bond 0.00877 / 0.44 ( 3) SS BOND : angle 1.12450 / 0.65 ( 6) hydrogen bonds : bond 0.04839 / 2.99 ( 53) hydrogen bonds : angle 6.64628 / 4.72 ( 156) link_NAG-ASN : bond 0.00482 / 0.30 ( 12) link_NAG-ASN : angle 2.73347 / 1.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.120 Fit side-chains REVERT: A 184 ILE cc_start: 0.3993 (OUTLIER) cc_final: 0.3471 (pp) REVERT: A 207 MET cc_start: 0.1711 (tpt) cc_final: 0.1407 (tmt) REVERT: A 219 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.4163 (pt) REVERT: A 236 TYR cc_start: 0.6105 (OUTLIER) cc_final: 0.3523 (t80) outliers start: 22 outliers final: 15 residues processed: 86 average time/residue: 0.3007 time to fit residues: 26.8850 Evaluate side-chains 90 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 242 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 = 0.5621 r_free = 0.5621 target = 0.309506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5990 r_free = 0.5990 target = 0.275187 restraints weight = 37071.689| |-----------------------------------------------------------------------------| r_work (start): 0.5532 rms_B_bonded: 5.33 r_work: 0.5876 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.5876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5504 r_free = 0.5504 target_work(ls_wunit_k1) = 0.293 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5504 r_free = 0.5504 target_work(ls_wunit_k1) = 0.293 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.5504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 1.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3531 Z= 0.225 Angle : 1.030 11.116 4830 Z= 0.529 Chirality : 0.063 0.276 606 Planarity : 0.004 0.029 579 Dihedral : 6.736 22.034 459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.25 % Allowed : 34.65 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 247 TYR 0.022 0.002 TYR C 125 PHE 0.022 0.003 PHE A 237 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 3516) covalent geometry : angle 1.00356 / 0.52 ( 4788) SS BOND : bond 0.00948 / 0.47 ( 3) SS BOND : angle 1.18283 / 0.69 ( 6) hydrogen bonds : bond 0.05000 / 3.11 ( 53) hydrogen bonds : angle 6.91358 / 4.92 ( 156) link_NAG-ASN : bond 0.00502 / 0.31 ( 12) link_NAG-ASN : angle 2.84669 / 1.78 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.143 Fit side-chains REVERT: A 184 ILE cc_start: 0.3889 (OUTLIER) cc_final: 0.3364 (pp) REVERT: A 207 MET cc_start: 0.1521 (tpt) cc_final: 0.1215 (tmt) REVERT: A 219 ILE cc_start: 0.4234 (OUTLIER) cc_final: 0.4024 (pt) REVERT: A 236 TYR cc_start: 0.6044 (OUTLIER) cc_final: 0.3507 (t80) outliers start: 20 outliers final: 15 residues processed: 82 average time/residue: 0.2815 time to fit residues: 24.1095 Evaluate side-chains 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.0010 overall best weight: 1.1926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5651 r_free = 0.5651 target = 0.316841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.6037 r_free = 0.6037 target = 0.282605 restraints weight = 33263.999| |-----------------------------------------------------------------------------| r_work (start): 0.5562 rms_B_bonded: 5.31 r_work: 0.5907 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.5907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5534 r_free = 0.5534 target_work(ls_wunit_k1) = 0.300 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5534 r_free = 0.5534 target_work(ls_wunit_k1) = 0.300 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.5534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 1.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3531 Z= 0.168 Angle : 0.983 12.744 4830 Z= 0.497 Chirality : 0.061 0.253 606 Planarity : 0.004 0.029 579 Dihedral : 6.379 22.000 459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 4.20 % Allowed : 36.48 % Favored : 59.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 180 TYR 0.015 0.001 TYR B 125 PHE 0.023 0.003 PHE A 237 HIS 0.008 0.003 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 3516) covalent geometry : angle 0.96410 / 0.49 ( 4788) SS BOND : bond 0.00617 / 0.31 ( 3) SS BOND : angle 0.72542 / 0.40 ( 6) hydrogen bonds : bond 0.04551 / 2.86 ( 53) hydrogen bonds : angle 6.75402 / 4.78 ( 156) link_NAG-ASN : bond 0.00505 / 0.32 ( 12) link_NAG-ASN : angle 2.44846 / 1.54 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.72 seconds wall clock time: 24 minutes 3.43 seconds (1443.43 seconds total)