Starting phenix.real_space_refine on Wed Jul 1 22:34:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.map" model { file = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u11_26274/07_2026/7u11_26274.cif" } resolution = 3.2 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= 0.000 sd= 0.004 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 9 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: 1.37, per 1000 atoms: 0.40 Number of scatterers: 3456 At special positions: 0 Unit cell: (106.326, 99.882, 32.22, 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=2.03 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: 0.25 Conformation dependent library (CDL) restraints added in 207.5 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, 62.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.490A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137 removed outlier: 6.406A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N TYR B 132 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 131 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER B 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ASP B 136 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N TYR A 135 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYR C 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ALA B 131 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER C 134 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N VAL B 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASP C 136 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TYR B 135 " --> pdb=" O ASP C 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 165 removed outlier: 6.354A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN B 145 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LEU A 144 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR B 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ILE A 146 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR B 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASN A 148 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN B 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU A 150 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR B 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N ASN B 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASN A 154 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N TYR B 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N SER B 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N TYR A 158 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLU B 161 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A 160 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N GLU B 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 162 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE B 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASN A 164 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN C 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N LEU B 144 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR C 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ILE B 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N THR C 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ASN B 148 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ASN C 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LEU B 150 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N THR C 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N ILE B 152 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N ASN C 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASN B 154 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N TYR C 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ASN B 156 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N SER C 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N TYR B 158 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N GLU C 161 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 160 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU C 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 162 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE C 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.589A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.582A 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 185 through 187 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 6.797A pdb=" N ILE A 195 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP B 196 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A 197 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 198 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 195 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP C 196 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR B 197 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR C 198 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.376A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.426A 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: 6.244A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS B 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE A 213 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N LEU B 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N THR A 215 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N SER B 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE A 217 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR B 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP C 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS C 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N PHE B 213 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU C 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N THR B 215 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N SER C 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N ILE B 217 " --> pdb=" O SER C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 224 through 228 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.593A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B 234 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE C 237 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR B 236 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS C 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY B 238 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLU C 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLN C 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER B 244 " --> pdb=" O GLN C 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253 40 hydrogen bonds defined for protein. 120 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: 0.44 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1053 1.34 - 1.46: 810 1.46 - 1.58: 1617 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 3516 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 NAG C 304 " pdb=" O5 NAG C 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1 NAG B 304 " pdb=" O5 NAG B 304 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CG LEU B 226 " pdb=" CD2 LEU B 226 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.09e+00 bond pdb=" CG LEU C 226 " pdb=" CD2 LEU C 226 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.09e+00 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 4356 1.19 - 2.37: 355 2.37 - 3.56: 56 3.56 - 4.74: 12 4.74 - 5.93: 9 Bond angle restraints: 4788 Sorted by residual: angle pdb=" N THR B 231 " pdb=" CA THR B 231 " pdb=" C THR B 231 " ideal model delta sigma weight residual 108.34 111.85 -3.51 1.31e+00 5.83e-01 7.18e+00 angle pdb=" N THR A 231 " pdb=" CA THR A 231 " pdb=" C THR A 231 " ideal model delta sigma weight residual 108.34 111.84 -3.50 1.31e+00 5.83e-01 7.12e+00 angle pdb=" N THR C 231 " pdb=" CA THR C 231 " pdb=" C THR C 231 " ideal model delta sigma weight residual 108.34 111.78 -3.44 1.31e+00 5.83e-01 6.90e+00 angle pdb=" CA TYR A 158 " pdb=" CB TYR A 158 " pdb=" CG TYR A 158 " ideal model delta sigma weight residual 113.90 118.60 -4.70 1.80e+00 3.09e-01 6.82e+00 angle pdb=" CA TYR C 158 " pdb=" CB TYR C 158 " pdb=" CG TYR C 158 " ideal model delta sigma weight residual 113.90 118.60 -4.70 1.80e+00 3.09e-01 6.81e+00 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 1822 16.07 - 32.14: 128 32.14 - 48.20: 54 48.20 - 64.27: 9 64.27 - 80.34: 6 Dihedral angle restraints: 2019 sinusoidal: 786 harmonic: 1233 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 140.13 -47.13 1 1.00e+01 1.00e-02 3.07e+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 93.00 140.13 -47.13 1 1.00e+01 1.00e-02 3.07e+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 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 486 0.071 - 0.142: 111 0.142 - 0.213: 3 0.213 - 0.285: 0 0.285 - 0.356: 6 Chirality restraints: 606 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 183 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 183 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C1 NAG A 301 " pdb=" ND2 ASN A 183 " pdb=" C2 NAG A 301 " pdb=" O5 NAG A 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 199 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 200 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 199 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 200 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO B 200 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.022 5.00e-02 4.00e+02 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 99 2.73 - 3.27: 3252 3.27 - 3.81: 5670 3.81 - 4.36: 6339 4.36 - 4.90: 12507 Nonbonded interactions: 27867 Sorted by model distance: nonbonded pdb=" OE2 GLU A 161 " pdb=" ND1 HIS A 239 " model vdw 2.186 3.120 nonbonded pdb=" OE2 GLU B 161 " pdb=" ND1 HIS B 239 " model vdw 2.186 3.120 nonbonded pdb=" OE2 GLU C 161 " pdb=" ND1 HIS C 239 " model vdw 2.187 3.120 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.316 3.120 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.317 3.120 ... (remaining 27862 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: 4.080 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: 0.020 Process input model: 5.510 Find NCS groups from input model: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 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 : 0.006 0.094 3531 Z= 0.246 Angle : 0.844 11.447 4830 Z= 0.405 Chirality : 0.062 0.356 606 Planarity : 0.004 0.040 579 Dihedral : 14.658 80.339 1224 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.36 % Allowed : 1.57 % Favored : 96.06 % 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: -2.79 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.017 0.002 TYR B 143 PHE 0.007 0.001 PHE B 237 HIS 0.005 0.002 HIS C 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 ( 3516) covalent geometry : angle 0.73149 / 0.38 ( 4788) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.99349 / 0.53 ( 6) hydrogen bonds : bond 0.05586 / 3.60 ( 40) hydrogen bonds : angle 5.54139 / 3.79 ( 120) link_NAG-ASN : bond 0.00601 / 0.38 ( 12) link_NAG-ASN : angle 4.92894 / 3.34 ( 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 44 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.109 Fit side-chains REVERT: A 207 MET cc_start: 0.3761 (OUTLIER) cc_final: 0.3503 (tpp) REVERT: A 220 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7728 (mtpp) REVERT: B 207 MET cc_start: 0.3907 (OUTLIER) cc_final: 0.3649 (tpt) REVERT: C 207 MET cc_start: 0.4592 (OUTLIER) cc_final: 0.4315 (tpp) REVERT: C 220 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7881 (tttm) outliers start: 9 outliers final: 0 residues processed: 39 average time/residue: 0.0536 time to fit residues: 2.7362 Evaluate side-chains 29 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 220 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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 = 0.5263 r_free = 0.5263 target = 0.220296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.195014 restraints weight = 11768.052| |-----------------------------------------------------------------------------| r_work (start): 0.4914 rms_B_bonded: 4.17 r_work: 0.4757 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4754 r_free = 0.4754 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4754 r_free = 0.4754 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3531 Z= 0.204 Angle : 0.896 11.063 4830 Z= 0.415 Chirality : 0.061 0.353 606 Planarity : 0.004 0.028 579 Dihedral : 7.560 34.042 476 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.57 % Allowed : 7.35 % Favored : 91.08 % 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: -2.90 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 180 TYR 0.021 0.003 TYR A 143 PHE 0.013 0.003 PHE B 171 HIS 0.007 0.003 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 3516) covalent geometry : angle 0.76305 / 0.39 ( 4788) SS BOND : bond 0.00100 / 0.05 ( 3) SS BOND : angle 0.81295 / 0.45 ( 6) hydrogen bonds : bond 0.02152 / 1.38 ( 40) hydrogen bonds : angle 4.26625 / 2.91 ( 120) link_NAG-ASN : bond 0.00970 / 0.61 ( 12) link_NAG-ASN : angle 5.49665 / 3.68 ( 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 37 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 34 average time/residue: 0.0349 time to fit residues: 1.6982 Evaluate side-chains 31 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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 = 0.4986 r_free = 0.4986 target = 0.184801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.156822 restraints weight = 14402.778| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 4.86 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3531 Z= 0.193 Angle : 0.877 11.293 4830 Z= 0.413 Chirality : 0.060 0.308 606 Planarity : 0.004 0.022 579 Dihedral : 6.393 20.302 459 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.36 % Allowed : 8.14 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.09 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.023 0.002 TYR A 143 PHE 0.013 0.003 PHE B 171 HIS 0.010 0.003 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 3516) covalent geometry : angle 0.74778 / 0.38 ( 4788) SS BOND : bond 0.00088 / 0.04 ( 3) SS BOND : angle 0.44211 / 0.25 ( 6) hydrogen bonds : bond 0.02006 / 1.23 ( 40) hydrogen bonds : angle 4.01904 / 2.72 ( 120) link_NAG-ASN : bond 0.00755 / 0.50 ( 12) link_NAG-ASN : angle 5.36251 / 3.59 ( 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 40 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.6614 (tp40) cc_final: 0.6317 (tp40) REVERT: B 247 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.7039 (ptm160) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.0425 time to fit residues: 2.1904 Evaluate side-chains 35 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 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 = 0.4973 r_free = 0.4973 target = 0.183884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.157549 restraints weight = 8572.851| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 3.92 r_work: 0.4569 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4556 r_free = 0.4556 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4556 r_free = 0.4556 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3531 Z= 0.173 Angle : 0.860 10.641 4830 Z= 0.403 Chirality : 0.059 0.336 606 Planarity : 0.003 0.018 579 Dihedral : 6.321 20.487 459 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.57 % Allowed : 12.07 % Favored : 86.35 % 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: -3.16 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.021 0.002 TYR A 143 PHE 0.012 0.002 PHE B 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 3516) covalent geometry : angle 0.73687 / 0.38 ( 4788) SS BOND : bond 0.00323 / 0.16 ( 3) SS BOND : angle 0.58956 / 0.33 ( 6) hydrogen bonds : bond 0.01827 / 1.08 ( 40) hydrogen bonds : angle 4.14388 / 2.85 ( 120) link_NAG-ASN : bond 0.00728 / 0.48 ( 12) link_NAG-ASN : angle 5.19499 / 3.50 ( 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 37 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: B 247 ARG cc_start: 0.7233 (ptm-80) cc_final: 0.6963 (ptm160) outliers start: 6 outliers final: 6 residues processed: 35 average time/residue: 0.0457 time to fit residues: 2.2155 Evaluate side-chains 32 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 168 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.182139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.154055 restraints weight = 13825.255| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 4.85 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4702 r_free = 0.4702 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4701 r_free = 0.4701 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3531 Z= 0.177 Angle : 0.862 10.515 4830 Z= 0.407 Chirality : 0.060 0.329 606 Planarity : 0.003 0.027 579 Dihedral : 6.229 19.753 459 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.89 % Allowed : 12.07 % Favored : 85.04 % 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: -3.16 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.021 0.002 TYR A 143 PHE 0.012 0.002 PHE B 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 3516) covalent geometry : angle 0.74259 / 0.38 ( 4788) SS BOND : bond 0.00019 / 0.01 ( 3) SS BOND : angle 0.80062 / 0.36 ( 6) hydrogen bonds : bond 0.01869 / 1.21 ( 40) hydrogen bonds : angle 4.21286 / 2.91 ( 120) link_NAG-ASN : bond 0.00683 / 0.46 ( 12) link_NAG-ASN : angle 5.11329 / 3.40 ( 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 42 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.5478 (tpp) cc_final: 0.5090 (ttt) REVERT: B 247 ARG cc_start: 0.7336 (ptm-80) cc_final: 0.7065 (ptm160) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 0.0387 time to fit residues: 1.9922 Evaluate side-chains 37 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.5028 r_free = 0.5028 target = 0.192032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.165983 restraints weight = 9942.457| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 4.11 r_work: 0.4595 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4576 r_free = 0.4576 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4576 r_free = 0.4576 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3531 Z= 0.135 Angle : 0.751 9.755 4830 Z= 0.356 Chirality : 0.058 0.289 606 Planarity : 0.003 0.035 579 Dihedral : 5.753 19.127 459 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.05 % Allowed : 14.44 % Favored : 84.51 % 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: -3.21 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.018 0.002 TYR A 143 PHE 0.010 0.002 PHE B 171 HIS 0.006 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3516) covalent geometry : angle 0.65106 / 0.33 ( 4788) SS BOND : bond 0.00032 / 0.02 ( 3) SS BOND : angle 0.59828 / 0.29 ( 6) hydrogen bonds : bond 0.01627 / 0.99 ( 40) hydrogen bonds : angle 4.14164 / 2.88 ( 120) link_NAG-ASN : bond 0.00679 / 0.44 ( 12) link_NAG-ASN : angle 4.39682 / 2.94 ( 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 34 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.0345 time to fit residues: 1.6760 Evaluate side-chains 33 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.4979 r_free = 0.4979 target = 0.185145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.156840 restraints weight = 15731.302| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 4.99 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3531 Z= 0.155 Angle : 0.789 9.596 4830 Z= 0.374 Chirality : 0.059 0.321 606 Planarity : 0.003 0.039 579 Dihedral : 5.924 19.666 459 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.84 % Allowed : 14.70 % Favored : 83.46 % 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: -3.23 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.018 0.002 TYR A 143 PHE 0.011 0.002 PHE A 171 HIS 0.006 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3516) covalent geometry : angle 0.68508 / 0.35 ( 4788) SS BOND : bond 0.00034 / 0.02 ( 3) SS BOND : angle 0.65665 / 0.31 ( 6) hydrogen bonds : bond 0.01671 / 1.05 ( 40) hydrogen bonds : angle 4.15001 / 2.85 ( 120) link_NAG-ASN : bond 0.00662 / 0.43 ( 12) link_NAG-ASN : angle 4.59034 / 3.05 ( 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 34 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 31 average time/residue: 0.0294 time to fit residues: 1.3811 Evaluate side-chains 34 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.4890 r_free = 0.4890 target = 0.176586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.148856 restraints weight = 11942.982| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 4.53 r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3531 Z= 0.191 Angle : 0.862 10.328 4830 Z= 0.412 Chirality : 0.060 0.332 606 Planarity : 0.004 0.042 579 Dihedral : 6.472 20.667 459 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.10 % Allowed : 15.22 % Favored : 82.68 % 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: -3.40 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 140 TYR 0.024 0.002 TYR A 143 PHE 0.013 0.002 PHE B 171 HIS 0.009 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 3516) covalent geometry : angle 0.74844 / 0.39 ( 4788) SS BOND : bond 0.00073 / 0.04 ( 3) SS BOND : angle 0.61265 / 0.32 ( 6) hydrogen bonds : bond 0.01935 / 1.22 ( 40) hydrogen bonds : angle 4.25272 / 2.91 ( 120) link_NAG-ASN : bond 0.00649 / 0.43 ( 12) link_NAG-ASN : angle 5.00904 / 3.31 ( 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 44 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: B 247 ARG cc_start: 0.7393 (ptm-80) cc_final: 0.7109 (ptm160) REVERT: C 135 TYR cc_start: 0.5925 (OUTLIER) cc_final: 0.4741 (m-10) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.0423 time to fit residues: 2.2369 Evaluate side-chains 37 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.4902 r_free = 0.4902 target = 0.178031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.152053 restraints weight = 8971.895| |-----------------------------------------------------------------------------| r_work (start): 0.4657 rms_B_bonded: 3.95 r_work: 0.4511 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3531 Z= 0.185 Angle : 0.842 9.843 4830 Z= 0.403 Chirality : 0.060 0.306 606 Planarity : 0.004 0.046 579 Dihedral : 6.194 19.959 459 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 1.57 % Allowed : 16.01 % Favored : 82.41 % 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: -3.42 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 140 TYR 0.023 0.002 TYR A 143 PHE 0.013 0.002 PHE A 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 3516) covalent geometry : angle 0.73528 / 0.38 ( 4788) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 0.67925 / 0.34 ( 6) hydrogen bonds : bond 0.01809 / 1.13 ( 40) hydrogen bonds : angle 4.24838 / 2.90 ( 120) link_NAG-ASN : bond 0.00644 / 0.43 ( 12) link_NAG-ASN : angle 4.80646 / 3.21 ( 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 42 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 ARG cc_start: 0.7323 (ptm-80) cc_final: 0.7016 (ptm160) REVERT: C 135 TYR cc_start: 0.6187 (OUTLIER) cc_final: 0.5080 (m-10) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.0482 time to fit residues: 2.5332 Evaluate side-chains 41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 = 0.4907 r_free = 0.4907 target = 0.178768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.150663 restraints weight = 14496.585| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 4.87 r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4636 r_free = 0.4636 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4636 r_free = 0.4636 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3531 Z= 0.175 Angle : 0.824 9.629 4830 Z= 0.395 Chirality : 0.060 0.307 606 Planarity : 0.004 0.051 579 Dihedral : 6.103 19.763 459 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.57 % Allowed : 16.27 % Favored : 82.15 % 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: -3.42 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 140 TYR 0.022 0.002 TYR A 143 PHE 0.013 0.002 PHE B 171 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 3516) covalent geometry : angle 0.72187 / 0.37 ( 4788) SS BOND : bond 0.00133 / 0.07 ( 3) SS BOND : angle 0.61191 / 0.34 ( 6) hydrogen bonds : bond 0.01803 / 1.11 ( 40) hydrogen bonds : angle 4.26373 / 2.91 ( 120) link_NAG-ASN : bond 0.00628 / 0.42 ( 12) link_NAG-ASN : angle 4.65653 / 3.10 ( 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 42 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.5118 (m-10) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.0346 time to fit residues: 1.9308 Evaluate side-chains 41 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 THR 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: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN B 154 ASN C 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.186289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.158037 restraints weight = 13356.084| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 4.86 r_work (final): 0.4721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4720 r_free = 0.4720 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4720 r_free = 0.4720 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3531 Z= 0.117 Angle : 0.720 8.867 4830 Z= 0.342 Chirality : 0.057 0.280 606 Planarity : 0.004 0.051 579 Dihedral : 5.563 18.057 459 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.05 % Allowed : 16.27 % Favored : 82.68 % 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: -3.33 (0.36), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.013 0.001 TYR A 158 PHE 0.009 0.001 PHE B 237 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3516) covalent geometry : angle 0.63010 / 0.32 ( 4788) SS BOND : bond 0.00077 / 0.04 ( 3) SS BOND : angle 0.57297 / 0.27 ( 6) hydrogen bonds : bond 0.01571 / 0.95 ( 40) hydrogen bonds : angle 4.18706 / 2.87 ( 120) link_NAG-ASN : bond 0.00700 / 0.46 ( 12) link_NAG-ASN : angle 4.09446 / 2.73 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.79 seconds wall clock time: 16 minutes 8.61 seconds (968.61 seconds total)