Starting phenix.real_space_refine on Wed Jul 1 22:33:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u12_26275/07_2026/7u12_26275.cif" } resolution = 3.5 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= 0.002 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 1 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: 1.46, per 1000 atoms: 0.42 Number of scatterers: 3456 At special positions: 0 Unit cell: (98.808, 118.14, 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=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.04 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: 0.27 Conformation dependent library (CDL) restraints added in 204.5 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, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125 removed outlier: 6.633A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (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: 9.036A pdb=" N SER A 130 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N VAL B 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 132 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR B 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N SER B 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N VAL C 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR B 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR C 135 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165 removed outlier: 5.950A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN B 145 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N LEU A 144 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR B 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ILE A 146 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N THR B 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ASN A 148 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ASN B 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU A 150 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N THR B 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASN B 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N ASN A 154 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N TYR B 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N ASN A 156 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N SER B 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N TYR A 158 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N GLU B 161 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 160 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU B 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 162 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE B 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASN A 164 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N LEU B 144 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ILE B 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR C 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN B 148 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N ASN C 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU B 150 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR C 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ILE B 152 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ASN C 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN B 154 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N TYR C 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ASN B 156 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N SER C 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N TYR B 158 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 10.323A pdb=" N GLU C 161 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 160 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLU C 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 162 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE C 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 5.752A 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: 6.575A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.568A 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198 removed outlier: 8.946A pdb=" N MET A 192 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ILE B 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN A 194 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR B 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 196 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N MET B 192 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ILE C 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN B 194 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N TYR C 197 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.405A 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: 6.452A pdb=" N VAL A 202 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.502A 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: 6.952A pdb=" N MET A 210 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR B 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP A 212 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.025A 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: 6.991A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245 removed outlier: 6.422A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 234 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE C 237 " --> pdb=" O THR B 234 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 236 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N HIS C 239 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 238 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU C 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN C 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 6.118A 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 removed outlier: 6.309A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 36 hydrogen bonds defined for protein. 108 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: 0.45 Time building geometry restraints manager: 0.37 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: 1051 1.34 - 1.46: 685 1.46 - 1.57: 1741 1.57 - 1.69: 3 1.69 - 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 1.253 0.250 3.40e-02 8.65e+02 5.40e+01 bond pdb=" CG PRO A 189 " pdb=" CD PRO A 189 " ideal model delta sigma weight residual 1.503 1.253 0.250 3.40e-02 8.65e+02 5.39e+01 bond pdb=" CG PRO B 189 " pdb=" CD PRO B 189 " ideal model delta sigma weight residual 1.503 1.255 0.248 3.40e-02 8.65e+02 5.34e+01 bond pdb=" CB PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 1.492 1.669 -0.177 5.00e-02 4.00e+02 1.26e+01 bond pdb=" CB PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 1.492 1.669 -0.177 5.00e-02 4.00e+02 1.25e+01 ... (remaining 3511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 4668 2.78 - 5.55: 90 5.55 - 8.33: 24 8.33 - 11.10: 3 11.10 - 13.88: 3 Bond angle restraints: 4788 Sorted by residual: angle pdb=" N PRO C 189 " pdb=" CD PRO C 189 " pdb=" CG PRO C 189 " ideal model delta sigma weight residual 103.20 89.32 13.88 1.50e+00 4.44e-01 8.56e+01 angle pdb=" N PRO A 189 " pdb=" CD PRO A 189 " pdb=" CG PRO A 189 " ideal model delta sigma weight residual 103.20 89.34 13.86 1.50e+00 4.44e-01 8.53e+01 angle pdb=" N PRO B 189 " pdb=" CD PRO B 189 " pdb=" CG PRO B 189 " ideal model delta sigma weight residual 103.20 89.37 13.83 1.50e+00 4.44e-01 8.50e+01 angle pdb=" N PHE A 171 " pdb=" CA PHE A 171 " pdb=" C PHE A 171 " ideal model delta sigma weight residual 108.96 115.81 -6.85 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N PHE B 171 " pdb=" CA PHE B 171 " pdb=" C PHE B 171 " ideal model delta sigma weight residual 108.96 115.78 -6.82 1.49e+00 4.50e-01 2.10e+01 ... (remaining 4783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1749 16.69 - 33.37: 171 33.37 - 50.06: 73 50.06 - 66.74: 17 66.74 - 83.43: 9 Dihedral angle restraints: 2019 sinusoidal: 786 harmonic: 1233 Sorted by residual: 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 30.37 62.63 1 1.00e+01 1.00e-02 5.19e+01 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 30.37 62.63 1 1.00e+01 1.00e-02 5.19e+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 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 474 0.081 - 0.162: 111 0.162 - 0.243: 15 0.243 - 0.324: 3 0.324 - 0.405: 3 Chirality restraints: 606 Sorted by residual: chirality pdb=" CG LEU A 226 " pdb=" CB LEU A 226 " pdb=" CD1 LEU A 226 " pdb=" CD2 LEU A 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CG LEU B 226 " pdb=" CB LEU B 226 " pdb=" CD1 LEU B 226 " pdb=" CD2 LEU B 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CG LEU C 226 " pdb=" CB LEU C 226 " pdb=" CD1 LEU C 226 " pdb=" CD2 LEU C 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 603 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 125 " -0.004 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR A 125 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 125 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 125 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 125 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 125 " -0.005 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR C 125 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR C 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 125 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR C 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 125 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 125 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " -0.004 2.00e-02 2.50e+03 2.39e-02 1.15e+01 pdb=" CG TYR B 125 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.007 2.00e-02 2.50e+03 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 86 2.71 - 3.26: 3290 3.26 - 3.80: 5387 3.80 - 4.35: 6630 4.35 - 4.90: 12470 Nonbonded interactions: 27863 Sorted by model distance: nonbonded pdb=" OG1 THR A 215 " pdb=" OD1 ASP B 212 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR B 215 " pdb=" OD1 ASP C 212 " model vdw 2.214 3.040 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.277 3.120 nonbonded pdb=" NZ LYS C 129 " pdb=" OD2 ASP C 136 " model vdw 2.279 3.120 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.279 3.120 ... (remaining 27858 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.010 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4488 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 : 0.011 0.250 3531 Z= 0.376 Angle : 1.183 13.880 4830 Z= 0.632 Chirality : 0.072 0.405 606 Planarity : 0.008 0.081 579 Dihedral : 17.185 83.426 1224 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.51 % Allowed : 2.36 % Favored : 92.13 % 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: -3.00 (0.37), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 140 TYR 0.050 0.004 TYR C 125 PHE 0.045 0.007 PHE B 171 HIS 0.003 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.01092 / 0.38 ( 3516) covalent geometry : angle 1.06082 / 0.61 ( 4788) SS BOND : bond 0.00774 / 0.39 ( 3) SS BOND : angle 3.85040 / 2.08 ( 6) hydrogen bonds : bond 0.15526 / 10.06 ( 36) hydrogen bonds : angle 8.72436 / 5.51 ( 108) link_NAG-ASN : bond 0.00867 / 0.57 ( 12) link_NAG-ASN : angle 5.95531 / 3.83 ( 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 130 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.135 Fit side-chains REVERT: A 178 LYS cc_start: 0.4567 (OUTLIER) cc_final: 0.3467 (mmpt) REVERT: C 178 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.4489 (pptt) REVERT: C 207 MET cc_start: 0.3545 (tmm) cc_final: 0.3187 (tmm) outliers start: 21 outliers final: 0 residues processed: 113 average time/residue: 0.0579 time to fit residues: 8.1476 Evaluate side-chains 73 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain C residue 178 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 HIS A 245 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5486 r_free = 0.5486 target = 0.321612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5632 r_free = 0.5632 target = 0.284315 restraints weight = 30915.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5582 r_free = 0.5582 target = 0.288320 restraints weight = 17163.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5592 r_free = 0.5592 target = 0.290033 restraints weight = 7482.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.290243 restraints weight = 6561.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.290616 restraints weight = 5128.889| |-----------------------------------------------------------------------------| r_work (final): 0.5429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5428 r_free = 0.5428 target_work(ls_wunit_k1) = 0.312 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5426 r_free = 0.5426 target_work(ls_wunit_k1) = 0.311 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.5426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 3531 Z= 0.244 Angle : 1.038 12.901 4830 Z= 0.506 Chirality : 0.060 0.373 606 Planarity : 0.005 0.034 579 Dihedral : 6.624 22.978 467 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.67 % Allowed : 13.91 % 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: -3.30 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 140 TYR 0.026 0.003 TYR A 132 PHE 0.021 0.004 PHE A 213 HIS 0.010 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 ( 3516) covalent geometry : angle 0.89127 / 0.47 ( 4788) SS BOND : bond 0.00936 / 0.47 ( 3) SS BOND : angle 3.08369 / 1.67 ( 6) hydrogen bonds : bond 0.04587 / 2.65 ( 36) hydrogen bonds : angle 6.91683 / 4.50 ( 108) link_NAG-ASN : bond 0.01152 / 0.76 ( 12) link_NAG-ASN : angle 6.09930 / 3.96 ( 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.156 Fit side-chains REVERT: A 228 MET cc_start: 0.6790 (tmm) cc_final: 0.5733 (tpp) REVERT: B 215 THR cc_start: 0.6167 (OUTLIER) cc_final: 0.5934 (m) REVERT: B 249 GLN cc_start: 0.6446 (tm-30) cc_final: 0.6234 (tm-30) REVERT: C 172 SER cc_start: 0.7760 (t) cc_final: 0.7310 (m) REVERT: C 223 ASN cc_start: 0.6099 (t0) cc_final: 0.5765 (t0) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.0477 time to fit residues: 6.3161 Evaluate side-chains 90 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5427 r_free = 0.5427 target = 0.311498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5592 r_free = 0.5592 target = 0.275583 restraints weight = 36131.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.279082 restraints weight = 16470.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5598 r_free = 0.5598 target = 0.279416 restraints weight = 6958.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5596 r_free = 0.5596 target = 0.279910 restraints weight = 5598.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5601 r_free = 0.5601 target = 0.280413 restraints weight = 5019.731| |-----------------------------------------------------------------------------| r_work (final): 0.5381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5380 r_free = 0.5380 target_work(ls_wunit_k1) = 0.285 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5380 r_free = 0.5380 target_work(ls_wunit_k1) = 0.285 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.5380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3531 Z= 0.204 Angle : 0.957 13.322 4830 Z= 0.456 Chirality : 0.058 0.346 606 Planarity : 0.004 0.027 579 Dihedral : 5.877 20.495 459 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.15 % Allowed : 19.95 % Favored : 76.90 % 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: -3.51 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.018 0.003 TYR B 250 PHE 0.023 0.003 PHE B 171 HIS 0.009 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 3516) covalent geometry : angle 0.79295 / 0.42 ( 4788) SS BOND : bond 0.01627 / 0.80 ( 3) SS BOND : angle 2.63504 / 1.41 ( 6) hydrogen bonds : bond 0.03113 / 1.96 ( 36) hydrogen bonds : angle 6.22216 / 4.08 ( 108) link_NAG-ASN : bond 0.01158 / 0.76 ( 12) link_NAG-ASN : angle 6.16712 / 3.96 ( 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 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.153 Fit side-chains REVERT: A 205 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5803 (pm20) REVERT: C 172 SER cc_start: 0.8369 (t) cc_final: 0.8049 (m) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.0375 time to fit residues: 4.9782 Evaluate side-chains 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 233 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.295201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5577 r_free = 0.5577 target = 0.256637 restraints weight = 17468.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5599 r_free = 0.5599 target = 0.258962 restraints weight = 7241.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5614 r_free = 0.5614 target = 0.260391 restraints weight = 4291.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5620 r_free = 0.5620 target = 0.261324 restraints weight = 3103.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.261770 restraints weight = 2504.446| |-----------------------------------------------------------------------------| r_work (final): 0.5299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5299 r_free = 0.5299 target_work(ls_wunit_k1) = 0.268 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5299 r_free = 0.5299 target_work(ls_wunit_k1) = 0.268 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.5299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.9220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3531 Z= 0.300 Angle : 1.106 12.986 4830 Z= 0.540 Chirality : 0.066 0.455 606 Planarity : 0.004 0.029 579 Dihedral : 6.919 26.526 459 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.99 % Allowed : 21.26 % Favored : 73.75 % 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: -3.80 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 180 TYR 0.025 0.004 TYR C 158 PHE 0.021 0.003 PHE B 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.30 ( 3516) covalent geometry : angle 0.94934 / 0.51 ( 4788) SS BOND : bond 0.01776 / 0.89 ( 3) SS BOND : angle 2.56949 / 1.41 ( 6) hydrogen bonds : bond 0.04518 / 3.14 ( 36) hydrogen bonds : angle 6.77073 / 4.38 ( 108) link_NAG-ASN : bond 0.01370 / 0.90 ( 12) link_NAG-ASN : angle 6.56493 / 4.20 ( 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 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.131 Fit side-chains REVERT: A 205 GLU cc_start: 0.6461 (mm-30) cc_final: 0.5969 (pm20) REVERT: A 209 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.5993 (m-10) REVERT: C 140 ARG cc_start: 0.3974 (OUTLIER) cc_final: 0.2741 (ptm-80) REVERT: C 172 SER cc_start: 0.8334 (t) cc_final: 0.8097 (m) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.0406 time to fit residues: 5.2645 Evaluate side-chains 94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 0.0670 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 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 = 0.5384 r_free = 0.5384 target = 0.303821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5589 r_free = 0.5589 target = 0.265731 restraints weight = 34162.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5576 r_free = 0.5576 target = 0.269668 restraints weight = 13838.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5582 r_free = 0.5582 target = 0.270239 restraints weight = 6027.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5580 r_free = 0.5580 target = 0.270400 restraints weight = 4955.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5583 r_free = 0.5583 target = 0.270527 restraints weight = 5139.947| |-----------------------------------------------------------------------------| r_work (final): 0.5324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5325 r_free = 0.5325 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5325 r_free = 0.5325 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.5325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.9390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3531 Z= 0.181 Angle : 0.942 13.462 4830 Z= 0.446 Chirality : 0.060 0.338 606 Planarity : 0.003 0.020 579 Dihedral : 5.837 24.828 459 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.46 % Allowed : 22.57 % Favored : 72.97 % 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: -3.77 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.016 0.002 TYR C 158 PHE 0.015 0.002 PHE B 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 3516) covalent geometry : angle 0.78507 / 0.41 ( 4788) SS BOND : bond 0.01257 / 0.63 ( 3) SS BOND : angle 2.63611 / 1.43 ( 6) hydrogen bonds : bond 0.03615 / 2.28 ( 36) hydrogen bonds : angle 6.38479 / 4.08 ( 108) link_NAG-ASN : bond 0.01240 / 0.83 ( 12) link_NAG-ASN : angle 5.99732 / 3.81 ( 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.126 Fit side-chains REVERT: A 135 TYR cc_start: 0.5923 (m-10) cc_final: 0.4878 (p90) REVERT: A 205 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5699 (pm20) REVERT: C 140 ARG cc_start: 0.4370 (OUTLIER) cc_final: 0.3327 (ptm-80) REVERT: C 172 SER cc_start: 0.8520 (t) cc_final: 0.8171 (m) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.0389 time to fit residues: 5.3936 Evaluate side-chains 95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE 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 3 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 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 = 0.5391 r_free = 0.5391 target = 0.303236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.263025 restraints weight = 22879.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5650 r_free = 0.5650 target = 0.265791 restraints weight = 8490.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5668 r_free = 0.5668 target = 0.267474 restraints weight = 4710.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.268540 restraints weight = 3265.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5682 r_free = 0.5682 target = 0.269269 restraints weight = 2612.399| |-----------------------------------------------------------------------------| r_work (final): 0.5346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5347 r_free = 0.5347 target_work(ls_wunit_k1) = 0.275 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5347 r_free = 0.5347 target_work(ls_wunit_k1) = 0.275 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.5347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.9839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3531 Z= 0.184 Angle : 0.957 13.094 4830 Z= 0.454 Chirality : 0.060 0.341 606 Planarity : 0.003 0.020 579 Dihedral : 5.760 20.239 459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.46 % Allowed : 23.36 % Favored : 72.18 % 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: -3.70 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.014 0.002 TYR C 158 PHE 0.016 0.003 PHE B 171 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 3516) covalent geometry : angle 0.80310 / 0.42 ( 4788) SS BOND : bond 0.00910 / 0.46 ( 3) SS BOND : angle 3.56038 / 2.08 ( 6) hydrogen bonds : bond 0.03874 / 2.35 ( 36) hydrogen bonds : angle 6.15028 / 3.85 ( 108) link_NAG-ASN : bond 0.01261 / 0.84 ( 12) link_NAG-ASN : angle 5.91749 / 3.78 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.5976 (m-10) cc_final: 0.4918 (p90) REVERT: A 205 GLU cc_start: 0.6362 (mm-30) cc_final: 0.5835 (pm20) REVERT: A 207 MET cc_start: 0.4383 (tmm) cc_final: 0.4132 (tmm) outliers start: 17 outliers final: 17 residues processed: 97 average time/residue: 0.0300 time to fit residues: 4.0946 Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 229 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5366 r_free = 0.5366 target = 0.298116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5570 r_free = 0.5570 target = 0.259670 restraints weight = 37828.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5539 r_free = 0.5539 target = 0.265156 restraints weight = 16769.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5541 r_free = 0.5541 target = 0.265639 restraints weight = 6187.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.266353 restraints weight = 6048.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.266305 restraints weight = 5408.215| |-----------------------------------------------------------------------------| r_work (final): 0.5319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5319 r_free = 0.5319 target_work(ls_wunit_k1) = 0.272 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5319 r_free = 0.5319 target_work(ls_wunit_k1) = 0.272 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.5319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 1.0421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3531 Z= 0.220 Angle : 1.006 12.636 4830 Z= 0.483 Chirality : 0.062 0.384 606 Planarity : 0.003 0.022 579 Dihedral : 6.025 22.520 459 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.77 % Allowed : 22.57 % Favored : 71.65 % 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: -3.84 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.016 0.003 TYR C 158 PHE 0.018 0.003 PHE A 237 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 ( 3516) covalent geometry : angle 0.85186 / 0.45 ( 4788) SS BOND : bond 0.00931 / 0.46 ( 3) SS BOND : angle 3.99051 / 2.32 ( 6) hydrogen bonds : bond 0.04024 / 2.47 ( 36) hydrogen bonds : angle 6.01486 / 3.71 ( 108) link_NAG-ASN : bond 0.01300 / 0.87 ( 12) link_NAG-ASN : angle 6.04774 / 3.87 ( 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 111 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.076 Fit side-chains REVERT: A 135 TYR cc_start: 0.6029 (m-10) cc_final: 0.5073 (p90) REVERT: A 205 GLU cc_start: 0.6482 (mm-30) cc_final: 0.5843 (pm20) REVERT: A 212 ASP cc_start: 0.6257 (t70) cc_final: 0.6042 (t70) REVERT: B 224 ILE cc_start: 0.6588 (mm) cc_final: 0.6383 (mm) REVERT: C 140 ARG cc_start: 0.4185 (OUTLIER) cc_final: 0.2814 (ptm-80) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.0371 time to fit residues: 5.0214 Evaluate side-chains 103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 229 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5404 r_free = 0.5404 target = 0.302059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5665 r_free = 0.5665 target = 0.262385 restraints weight = 29009.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.265521 restraints weight = 10121.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.266853 restraints weight = 6224.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5631 r_free = 0.5631 target = 0.267030 restraints weight = 4224.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5636 r_free = 0.5636 target = 0.267422 restraints weight = 4304.730| |-----------------------------------------------------------------------------| r_work (final): 0.5351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5352 r_free = 0.5352 target_work(ls_wunit_k1) = 0.275 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5352 r_free = 0.5352 target_work(ls_wunit_k1) = 0.275 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.5352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 1.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3531 Z= 0.182 Angle : 0.947 12.951 4830 Z= 0.450 Chirality : 0.059 0.318 606 Planarity : 0.003 0.020 579 Dihedral : 5.593 17.552 459 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.77 % Allowed : 22.83 % Favored : 71.39 % 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: -3.83 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.023 0.002 TYR A 143 PHE 0.014 0.002 PHE A 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 3516) covalent geometry : angle 0.80109 / 0.42 ( 4788) SS BOND : bond 0.00914 / 0.46 ( 3) SS BOND : angle 3.35572 / 1.94 ( 6) hydrogen bonds : bond 0.03741 / 2.22 ( 36) hydrogen bonds : angle 5.62777 / 3.43 ( 108) link_NAG-ASN : bond 0.01302 / 0.88 ( 12) link_NAG-ASN : angle 5.76334 / 3.66 ( 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 112 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6014 (m-10) cc_final: 0.4961 (p90) REVERT: A 205 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5790 (pm20) REVERT: A 207 MET cc_start: 0.4485 (tmm) cc_final: 0.4018 (tmm) REVERT: B 207 MET cc_start: 0.3513 (tpp) cc_final: 0.3286 (tpt) REVERT: B 224 ILE cc_start: 0.6396 (mm) cc_final: 0.6195 (mm) REVERT: C 140 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.2974 (ptm-80) REVERT: C 206 GLU cc_start: 0.5970 (tp30) cc_final: 0.4856 (pm20) outliers start: 22 outliers final: 19 residues processed: 105 average time/residue: 0.0292 time to fit residues: 4.1724 Evaluate side-chains 104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 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 16 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 229 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.301976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5637 r_free = 0.5637 target = 0.262056 restraints weight = 23052.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5666 r_free = 0.5666 target = 0.264890 restraints weight = 8607.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.266666 restraints weight = 4841.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5685 r_free = 0.5685 target = 0.267638 restraints weight = 3364.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5696 r_free = 0.5696 target = 0.268363 restraints weight = 2731.704| |-----------------------------------------------------------------------------| r_work (final): 0.5355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5355 r_free = 0.5355 target_work(ls_wunit_k1) = 0.276 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5355 r_free = 0.5355 target_work(ls_wunit_k1) = 0.276 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.5355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5750 moved from start: 1.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3531 Z= 0.185 Angle : 0.977 12.784 4830 Z= 0.467 Chirality : 0.059 0.315 606 Planarity : 0.003 0.016 579 Dihedral : 5.593 18.997 459 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.51 % Allowed : 24.67 % Favored : 69.82 % 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: -3.90 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.020 0.002 TYR A 143 PHE 0.015 0.003 PHE A 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 3516) covalent geometry : angle 0.82880 / 0.43 ( 4788) SS BOND : bond 0.00975 / 0.49 ( 3) SS BOND : angle 5.03930 / 2.98 ( 6) hydrogen bonds : bond 0.03790 / 2.27 ( 36) hydrogen bonds : angle 5.83072 / 3.60 ( 108) link_NAG-ASN : bond 0.01277 / 0.86 ( 12) link_NAG-ASN : angle 5.69135 / 3.63 ( 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.6070 (m-10) cc_final: 0.4936 (p90) REVERT: A 205 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5682 (pm20) REVERT: A 215 THR cc_start: 0.6817 (p) cc_final: 0.6431 (p) REVERT: C 140 ARG cc_start: 0.4268 (OUTLIER) cc_final: 0.2909 (ptm-80) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.0274 time to fit residues: 3.7910 Evaluate side-chains 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5389 r_free = 0.5389 target = 0.279584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5555 r_free = 0.5555 target = 0.252938 restraints weight = 37291.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.256366 restraints weight = 10593.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5617 r_free = 0.5617 target = 0.258435 restraints weight = 5123.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5625 r_free = 0.5625 target = 0.259666 restraints weight = 3331.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5626 r_free = 0.5626 target = 0.260261 restraints weight = 2535.702| |-----------------------------------------------------------------------------| r_work (final): 0.5336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5335 r_free = 0.5335 target_work(ls_wunit_k1) = 0.271 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5335 r_free = 0.5335 target_work(ls_wunit_k1) = 0.271 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.5335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 1.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3531 Z= 0.234 Angle : 1.050 12.496 4830 Z= 0.512 Chirality : 0.062 0.341 606 Planarity : 0.004 0.023 579 Dihedral : 5.849 24.005 459 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.30 % Allowed : 25.20 % Favored : 68.50 % 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: -4.07 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 140 TYR 0.021 0.003 TYR A 143 PHE 0.020 0.003 PHE A 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 3516) covalent geometry : angle 0.91411 / 0.48 ( 4788) SS BOND : bond 0.01015 / 0.51 ( 3) SS BOND : angle 4.12887 / 2.37 ( 6) hydrogen bonds : bond 0.03965 / 2.41 ( 36) hydrogen bonds : angle 5.56943 / 3.44 ( 108) link_NAG-ASN : bond 0.01339 / 0.89 ( 12) link_NAG-ASN : angle 5.82093 / 3.73 ( 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.130 Fit side-chains REVERT: A 135 TYR cc_start: 0.6134 (m-10) cc_final: 0.5017 (p90) REVERT: A 205 GLU cc_start: 0.6735 (mm-30) cc_final: 0.5814 (pm20) REVERT: C 140 ARG cc_start: 0.4034 (OUTLIER) cc_final: 0.2934 (ptm-80) outliers start: 24 outliers final: 18 residues processed: 99 average time/residue: 0.0368 time to fit residues: 4.9962 Evaluate side-chains 104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 0.0010 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5426 r_free = 0.5426 target = 0.306742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5709 r_free = 0.5709 target = 0.266668 restraints weight = 35607.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5618 r_free = 0.5618 target = 0.271687 restraints weight = 14475.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5610 r_free = 0.5610 target = 0.273343 restraints weight = 6421.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5615 r_free = 0.5615 target = 0.273661 restraints weight = 5656.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5617 r_free = 0.5617 target = 0.273768 restraints weight = 5630.546| |-----------------------------------------------------------------------------| r_work (final): 0.5376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5375 r_free = 0.5375 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5375 r_free = 0.5375 target_work(ls_wunit_k1) = 0.281 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.5375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 1.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3531 Z= 0.170 Angle : 0.977 12.807 4830 Z= 0.466 Chirality : 0.059 0.300 606 Planarity : 0.003 0.017 579 Dihedral : 5.572 18.272 459 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.99 % Allowed : 26.25 % Favored : 68.77 % 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: -3.92 (0.35), 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 ARG 0.002 0.001 ARG C 247 TYR 0.019 0.002 TYR A 143 PHE 0.015 0.003 PHE C 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 3516) covalent geometry : angle 0.84453 / 0.44 ( 4788) SS BOND : bond 0.00895 / 0.45 ( 3) SS BOND : angle 3.46680 / 1.97 ( 6) hydrogen bonds : bond 0.03592 / 2.08 ( 36) hydrogen bonds : angle 5.37174 / 3.35 ( 108) link_NAG-ASN : bond 0.01235 / 0.83 ( 12) link_NAG-ASN : angle 5.57554 / 3.56 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 784.03 seconds wall clock time: 14 minutes 15.20 seconds (855.20 seconds total)