Starting phenix.real_space_refine on Tue Feb 11 01:51:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_26276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_26276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_26276.map" model { file = "/net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_26276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u13_26276/02_2025/7u13_26276.cif" } resolution = 2.9 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.02, per 1000 atoms: 1.16 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: 0.83 Conformation dependent library (CDL) restraints added in 705.6 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: 0.45 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: 0.79 Time building geometry restraints manager: 0.98 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: 2068 26.07 - 52.13: 171 52.13 - 78.20: 18 78.20 - 104.27: 10 104.27 - 130.33: 4 Dihedral angle restraints: 2271 sinusoidal: 1038 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 2268 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.410 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.410 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4696 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 3516 Z= 1.157 Angle : 2.431 73.856 4788 Z= 1.083 Chirality : 0.071 0.358 606 Planarity : 0.006 0.049 579 Dihedral : 19.232 130.333 1476 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 (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: -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 HIS 0.003 0.002 HIS A 222 PHE 0.016 0.004 PHE A 171 TYR 0.033 0.005 TYR A 157 ARG 0.004 0.001 ARG C 247 *********************** 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 : 0.393 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: 0.9207 time to fit residues: 129.4794 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 : 0.344 ------------------------------------------------------------------------------- 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 32 optimal weight: 7.9990 chunk 29 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 229 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 242 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 = 0.5719 r_free = 0.5719 target = 0.331478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.6036 r_free = 0.6036 target = 0.294894 restraints weight = 31110.110| |-----------------------------------------------------------------------------| r_work (start): 0.5610 rms_B_bonded: 5.48 r_work: 0.5938 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.5938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5596 r_free = 0.5596 target_work(ls_wunit_k1) = 0.315 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5594 r_free = 0.5594 target_work(ls_wunit_k1) = 0.314 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3516 Z= 0.350 Angle : 0.959 9.893 4788 Z= 0.501 Chirality : 0.061 0.263 606 Planarity : 0.006 0.062 579 Dihedral : 15.719 107.772 729 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 7.87 % Allowed : 17.06 % Favored : 75.07 % 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: -3.56 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS A 239 PHE 0.011 0.002 PHE A 237 TYR 0.020 0.003 TYR C 248 ARG 0.002 0.001 ARG A 180 *********************** 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 117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4575 (mmm) cc_final: 0.2121 (ptt) REVERT: A 236 TYR cc_start: 0.5123 (p90) cc_final: 0.3635 (t80) REVERT: A 245 GLN cc_start: 0.6742 (mp10) cc_final: 0.6447 (tt0) REVERT: B 231 THR cc_start: 0.6384 (p) cc_final: 0.6132 (p) REVERT: C 125 TYR cc_start: 0.4931 (t80) cc_final: 0.3375 (p90) REVERT: C 126 ILE cc_start: 0.5825 (OUTLIER) cc_final: 0.5505 (mm) REVERT: C 216 LEU cc_start: 0.7668 (mm) cc_final: 0.7349 (tt) REVERT: C 250 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.4656 (p90) outliers start: 30 outliers final: 7 residues processed: 103 average time/residue: 0.8368 time to fit residues: 89.6287 Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 126 ILE 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 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5717 r_free = 0.5717 target = 0.329226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5992 r_free = 0.5992 target = 0.291539 restraints weight = 18814.150| |-----------------------------------------------------------------------------| r_work (start): 0.5589 rms_B_bonded: 4.38 r_work: 0.5946 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.5897 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.5897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5539 r_free = 0.5539 target_work(ls_wunit_k1) = 0.308 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5539 r_free = 0.5539 target_work(ls_wunit_k1) = 0.308 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3516 Z= 0.267 Angle : 0.905 10.803 4788 Z= 0.466 Chirality : 0.058 0.260 606 Planarity : 0.004 0.035 579 Dihedral : 13.909 105.862 713 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 5.77 % Allowed : 27.30 % Favored : 66.93 % 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: -3.51 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.012 0.002 PHE A 171 TYR 0.017 0.002 TYR A 125 ARG 0.001 0.000 ARG B 247 *********************** 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.4706 (mmm) cc_final: 0.2159 (ptt) REVERT: A 245 GLN cc_start: 0.6569 (mp10) cc_final: 0.6130 (tt0) REVERT: B 249 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.6102 (tt0) REVERT: C 216 LEU cc_start: 0.7282 (mm) cc_final: 0.6995 (tt) REVERT: C 250 TYR cc_start: 0.5461 (OUTLIER) cc_final: 0.4881 (p90) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 0.7785 time to fit residues: 81.0937 Evaluate side-chains 91 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 236 TYR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 233 THR 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 1 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.324818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5980 r_free = 0.5980 target = 0.286561 restraints weight = 24352.227| |-----------------------------------------------------------------------------| r_work (start): 0.5563 rms_B_bonded: 5.12 r_work: 0.5929 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.5879 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.5879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5507 r_free = 0.5507 target_work(ls_wunit_k1) = 0.303 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5507 r_free = 0.5507 target_work(ls_wunit_k1) = 0.303 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.5507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.8634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3516 Z= 0.288 Angle : 0.946 11.620 4788 Z= 0.483 Chirality : 0.060 0.270 606 Planarity : 0.004 0.026 579 Dihedral : 13.450 102.623 711 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 6.56 % Allowed : 28.35 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 239 PHE 0.010 0.002 PHE B 171 TYR 0.015 0.002 TYR A 125 ARG 0.001 0.000 ARG A 180 *********************** 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.1570 (tpt) cc_final: 0.0332 (tpt) REVERT: A 210 MET cc_start: 0.4962 (mmm) cc_final: 0.2456 (ptt) REVERT: A 245 GLN cc_start: 0.6689 (mp10) cc_final: 0.6282 (tt0) REVERT: B 249 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6169 (tt0) REVERT: C 250 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.5186 (p90) outliers start: 25 outliers final: 10 residues processed: 98 average time/residue: 0.8587 time to fit residues: 87.3636 Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 233 THR 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 B residue 236 TYR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 132 TYR 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 20 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5628 r_free = 0.5628 target = 0.312431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5954 r_free = 0.5954 target = 0.275858 restraints weight = 25421.329| |-----------------------------------------------------------------------------| r_work (start): 0.5524 rms_B_bonded: 4.63 r_work: 0.5903 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.5863 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.5863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5480 r_free = 0.5480 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 = 0.5480 r_free = 0.5480 target_work(ls_wunit_k1) = 0.293 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 1.0165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 3516 Z= 0.412 Angle : 1.076 11.254 4788 Z= 0.557 Chirality : 0.064 0.344 606 Planarity : 0.004 0.027 579 Dihedral : 14.361 101.589 711 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 7.35 % Allowed : 29.66 % Favored : 62.99 % 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: -4.09 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 239 PHE 0.026 0.003 PHE C 237 TYR 0.021 0.003 TYR B 250 ARG 0.003 0.001 ARG B 247 *********************** 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 100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.397 Fit side-chains REVERT: A 219 ILE cc_start: 0.4419 (OUTLIER) cc_final: 0.3923 (pp) REVERT: B 163 GLU cc_start: 0.5264 (mp0) cc_final: 0.4993 (mp0) REVERT: B 249 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6272 (tt0) REVERT: C 140 ARG cc_start: 0.4560 (OUTLIER) cc_final: 0.4003 (ppt90) REVERT: C 224 ILE cc_start: 0.4458 (OUTLIER) cc_final: 0.3226 (pp) outliers start: 28 outliers final: 11 residues processed: 89 average time/residue: 0.8900 time to fit residues: 82.2709 Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 THR 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 B residue 236 TYR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 233 THR 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 11 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5672 r_free = 0.5672 target = 0.320648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.6039 r_free = 0.6039 target = 0.285405 restraints weight = 31581.505| |-----------------------------------------------------------------------------| r_work (start): 0.5574 rms_B_bonded: 5.20 r_work: 0.5924 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.5924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5552 r_free = 0.5552 target_work(ls_wunit_k1) = 0.304 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5552 r_free = 0.5552 target_work(ls_wunit_k1) = 0.304 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 1.0249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3516 Z= 0.263 Angle : 0.939 11.902 4788 Z= 0.477 Chirality : 0.059 0.247 606 Planarity : 0.003 0.021 579 Dihedral : 13.394 100.832 711 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 4.99 % Allowed : 32.81 % Favored : 62.20 % 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: -3.97 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 239 PHE 0.020 0.003 PHE C 237 TYR 0.015 0.002 TYR A 125 ARG 0.001 0.000 ARG C 140 *********************** 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 93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.399 Fit side-chains REVERT: A 207 MET cc_start: 0.1598 (tpt) cc_final: 0.0436 (tpt) REVERT: A 245 GLN cc_start: 0.6572 (mp10) cc_final: 0.6099 (tt0) REVERT: C 132 TYR cc_start: 0.2980 (OUTLIER) cc_final: 0.2758 (t80) REVERT: C 242 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6007 (mt0) REVERT: C 250 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.5402 (p90) outliers start: 19 outliers final: 9 residues processed: 87 average time/residue: 0.8906 time to fit residues: 80.3700 Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 132 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 0.0060 chunk 6 optimal weight: 10.0000 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN B 138 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.311812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5938 r_free = 0.5938 target = 0.275303 restraints weight = 24548.384| |-----------------------------------------------------------------------------| r_work (start): 0.5512 rms_B_bonded: 4.45 r_work: 0.5897 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.5852 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.5852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5466 r_free = 0.5466 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 = 0.5466 r_free = 0.5466 target_work(ls_wunit_k1) = 0.292 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 1.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3516 Z= 0.357 Angle : 1.008 10.563 4788 Z= 0.513 Chirality : 0.062 0.288 606 Planarity : 0.004 0.024 579 Dihedral : 13.439 98.398 711 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.40 % Allowed : 30.71 % 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 (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: -4.11 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.018 0.003 PHE A 237 TYR 0.019 0.003 TYR C 125 ARG 0.002 0.000 ARG B 247 *********************** 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 103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.365 Fit side-chains REVERT: A 207 MET cc_start: 0.1879 (tpt) cc_final: 0.1649 (tmt) REVERT: A 219 ILE cc_start: 0.4422 (OUTLIER) cc_final: 0.3914 (pp) REVERT: C 242 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6104 (mt0) outliers start: 32 outliers final: 16 residues processed: 91 average time/residue: 0.7631 time to fit residues: 72.4439 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 MET 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 B residue 236 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 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 23 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 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 = 0.5646 r_free = 0.5646 target = 0.317192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5983 r_free = 0.5983 target = 0.280593 restraints weight = 31534.863| |-----------------------------------------------------------------------------| r_work (start): 0.5542 rms_B_bonded: 5.10 r_work: 0.5898 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.5898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5516 r_free = 0.5516 target_work(ls_wunit_k1) = 0.300 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5516 r_free = 0.5516 target_work(ls_wunit_k1) = 0.300 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 1.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3516 Z= 0.288 Angle : 0.975 11.749 4788 Z= 0.494 Chirality : 0.060 0.344 606 Planarity : 0.004 0.024 579 Dihedral : 12.966 99.059 711 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.25 % Allowed : 34.12 % Favored : 60.63 % 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: -4.10 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.028 0.003 PHE C 237 TYR 0.017 0.002 TYR A 125 ARG 0.002 0.000 ARG B 140 *********************** 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 93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.354 Fit side-chains REVERT: A 157 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5339 (t80) REVERT: A 219 ILE cc_start: 0.4089 (OUTLIER) cc_final: 0.3680 (pp) REVERT: A 236 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.3285 (t80) REVERT: A 245 GLN cc_start: 0.6753 (mp10) cc_final: 0.6103 (tt0) outliers start: 20 outliers final: 13 residues processed: 85 average time/residue: 0.8139 time to fit residues: 71.8711 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 219 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 130 SER Chi-restraints excluded: chain B residue 185 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 B residue 236 TYR Chi-restraints excluded: chain C residue 233 THR 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 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN C 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.320595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.6012 r_free = 0.6012 target = 0.285462 restraints weight = 24440.978| |-----------------------------------------------------------------------------| r_work (start): 0.5574 rms_B_bonded: 4.49 r_work: 0.5925 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.5891 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.5891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5510 r_free = 0.5510 target_work(ls_wunit_k1) = 0.299 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5510 r_free = 0.5510 target_work(ls_wunit_k1) = 0.299 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 1.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3516 Z= 0.269 Angle : 0.969 11.451 4788 Z= 0.487 Chirality : 0.059 0.255 606 Planarity : 0.004 0.029 579 Dihedral : 12.343 97.634 711 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.46 % Allowed : 35.43 % 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 (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: -4.00 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS A 239 PHE 0.023 0.003 PHE C 237 TYR 0.023 0.002 TYR B 250 ARG 0.001 0.000 ARG C 140 *********************** 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 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.356 Fit side-chains REVERT: A 157 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5388 (t80) REVERT: A 207 MET cc_start: 0.1857 (tpt) cc_final: 0.1480 (tmt) REVERT: A 219 ILE cc_start: 0.4184 (OUTLIER) cc_final: 0.3744 (pp) REVERT: A 228 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.3934 (tpt) REVERT: A 245 GLN cc_start: 0.6603 (mp10) cc_final: 0.6177 (tt0) REVERT: C 250 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.5292 (p90) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.8684 time to fit residues: 69.4501 Evaluate side-chains 79 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 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 B residue 236 TYR 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: 10.0000 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.0170 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.0040 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5673 r_free = 0.5673 target = 0.319581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.6067 r_free = 0.6067 target = 0.284661 restraints weight = 29547.097| |-----------------------------------------------------------------------------| r_work (start): 0.5574 rms_B_bonded: 5.31 r_work: 0.5920 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.5920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5537 r_free = 0.5537 target_work(ls_wunit_k1) = 0.302 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5537 r_free = 0.5537 target_work(ls_wunit_k1) = 0.302 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5522 moved from start: 1.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3516 Z= 0.279 Angle : 0.953 10.744 4788 Z= 0.481 Chirality : 0.058 0.252 606 Planarity : 0.003 0.030 579 Dihedral : 12.121 95.332 711 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % 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 (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: -3.93 (0.33), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.018 0.002 PHE A 237 TYR 0.021 0.002 TYR B 250 ARG 0.002 0.000 ARG B 140 ********************** 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 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.373 Fit side-chains REVERT: A 207 MET cc_start: 0.1493 (tpt) cc_final: 0.1109 (tmt) REVERT: A 219 ILE cc_start: 0.4069 (OUTLIER) cc_final: 0.3636 (pp) REVERT: A 245 GLN cc_start: 0.6590 (mp10) cc_final: 0.6108 (tt0) REVERT: C 250 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5115 (p90) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.8703 time to fit residues: 66.0219 Evaluate side-chains 78 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 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 B residue 236 TYR 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 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 0.2980 chunk 28 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 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 = 0.5657 r_free = 0.5657 target = 0.318135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.6036 r_free = 0.6036 target = 0.283294 restraints weight = 32640.992| |-----------------------------------------------------------------------------| r_work (start): 0.5553 rms_B_bonded: 5.53 r_work: 0.5888 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.5888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5516 r_free = 0.5516 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 = 0.5516 r_free = 0.5516 target_work(ls_wunit_k1) = 0.301 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 1.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3516 Z= 0.289 Angle : 0.974 10.833 4788 Z= 0.489 Chirality : 0.059 0.247 606 Planarity : 0.004 0.033 579 Dihedral : 11.978 93.487 711 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.46 % Allowed : 36.75 % Favored : 58.79 % 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: -3.97 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 239 PHE 0.029 0.003 PHE C 237 TYR 0.019 0.002 TYR B 250 ARG 0.001 0.000 ARG B 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.68 seconds wall clock time: 55 minutes 42.95 seconds (3342.95 seconds total)