Starting phenix.real_space_refine on Tue Mar 3 11:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u12_26275/03_2026/7u12_26275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u12_26275/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u12_26275/03_2026/7u12_26275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u12_26275/03_2026/7u12_26275.map" model { file = "/net/cci-nas-00/data/ceres_data/7u12_26275/03_2026/7u12_26275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u12_26275/03_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-5986/lib/python3.9/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.53, per 1000 atoms: 0.44 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: 0.25 Conformation dependent library (CDL) restraints added in 211.2 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: 0.12 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: 0.44 Time building geometry restraints manager: 0.32 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: 1965 16.69 - 33.37: 189 33.37 - 50.06: 91 50.06 - 66.74: 17 66.74 - 83.43: 9 Dihedral angle restraints: 2271 sinusoidal: 1038 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 2268 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4439 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 : 16.716 83.426 1476 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 covalent geometry : bond 0.01092 ( 3516) covalent geometry : angle 1.06082 ( 4788) SS BOND : bond 0.00774 ( 3) SS BOND : angle 3.85040 ( 6) hydrogen bonds : bond 0.15526 ( 36) hydrogen bonds : angle 8.72436 ( 108) link_NAG-ASN : bond 0.00867 ( 12) link_NAG-ASN : angle 5.95531 ( 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 : 0.124 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: 0.0613 time to fit residues: 8.5772 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 : 0.123 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.5488 r_free = 0.5488 target = 0.320977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5641 r_free = 0.5641 target = 0.283308 restraints weight = 30290.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5594 r_free = 0.5594 target = 0.287635 restraints weight = 16794.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.288909 restraints weight = 7259.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5603 r_free = 0.5603 target = 0.288993 restraints weight = 6702.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5606 r_free = 0.5606 target = 0.289396 restraints weight = 5320.896| |-----------------------------------------------------------------------------| r_work (final): 0.5431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5431 r_free = 0.5431 target_work(ls_wunit_k1) = 0.310 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5427 r_free = 0.5427 target_work(ls_wunit_k1) = 0.309 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 3531 Z= 0.248 Angle : 1.049 13.195 4830 Z= 0.510 Chirality : 0.062 0.445 606 Planarity : 0.005 0.034 579 Dihedral : 8.567 52.661 719 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.41 % Allowed : 14.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.34), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 140 TYR 0.026 0.003 TYR A 132 PHE 0.022 0.004 PHE A 213 HIS 0.011 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 3516) covalent geometry : angle 0.89758 ( 4788) SS BOND : bond 0.01065 ( 3) SS BOND : angle 3.06621 ( 6) hydrogen bonds : bond 0.04637 ( 36) hydrogen bonds : angle 6.96448 ( 108) link_NAG-ASN : bond 0.01174 ( 12) link_NAG-ASN : angle 6.24141 ( 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 111 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.126 Fit side-chains REVERT: A 228 MET cc_start: 0.6421 (tmm) cc_final: 0.5651 (tpp) REVERT: C 172 SER cc_start: 0.7747 (t) cc_final: 0.7290 (m) REVERT: C 223 ASN cc_start: 0.6092 (t0) cc_final: 0.5838 (t0) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.0478 time to fit residues: 6.3864 Evaluate side-chains 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 133 VAL 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 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: 9.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN C 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.280504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5494 r_free = 0.5494 target = 0.255619 restraints weight = 31448.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.259026 restraints weight = 8646.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.261027 restraints weight = 4138.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5557 r_free = 0.5557 target = 0.262209 restraints weight = 2720.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5556 r_free = 0.5556 target = 0.262794 restraints weight = 2105.709| |-----------------------------------------------------------------------------| r_work (final): 0.5297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5297 r_free = 0.5297 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 = 0.5297 r_free = 0.5297 target_work(ls_wunit_k1) = 0.272 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.8460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 3531 Z= 0.298 Angle : 1.121 12.780 4830 Z= 0.547 Chirality : 0.064 0.428 606 Planarity : 0.004 0.034 579 Dihedral : 10.207 56.364 711 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.51 % Allowed : 19.16 % Favored : 75.33 % 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: -3.71 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 180 TYR 0.026 0.004 TYR C 158 PHE 0.016 0.003 PHE A 237 HIS 0.008 0.003 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00685 ( 3516) covalent geometry : angle 0.96366 ( 4788) SS BOND : bond 0.02167 ( 3) SS BOND : angle 2.49357 ( 6) hydrogen bonds : bond 0.03898 ( 36) hydrogen bonds : angle 6.53302 ( 108) link_NAG-ASN : bond 0.01368 ( 12) link_NAG-ASN : angle 6.63080 ( 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 112 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.147 Fit side-chains REVERT: A 205 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5913 (pm20) REVERT: A 209 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5763 (m-10) REVERT: B 207 MET cc_start: 0.4038 (tmm) cc_final: 0.3764 (tmm) REVERT: B 249 GLN cc_start: 0.6222 (tm-30) cc_final: 0.6006 (tm-30) REVERT: C 140 ARG cc_start: 0.3817 (OUTLIER) cc_final: 0.3041 (ptm-80) outliers start: 21 outliers final: 13 residues processed: 103 average time/residue: 0.0456 time to fit residues: 6.2913 Evaluate side-chains 93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 209 TYR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain B residue 171 PHE 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 226 LEU 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: 9.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 HIS ** B 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 = 0.5354 r_free = 0.5354 target = 0.279484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5534 r_free = 0.5534 target = 0.255893 restraints weight = 17812.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5560 r_free = 0.5560 target = 0.258545 restraints weight = 6538.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5576 r_free = 0.5576 target = 0.260092 restraints weight = 3688.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5579 r_free = 0.5579 target = 0.261037 restraints weight = 2648.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.261686 restraints weight = 2169.776| |-----------------------------------------------------------------------------| r_work (final): 0.5310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5310 r_free = 0.5310 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 = 0.5310 r_free = 0.5310 target_work(ls_wunit_k1) = 0.271 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.9427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3531 Z= 0.243 Angle : 1.023 12.992 4830 Z= 0.492 Chirality : 0.063 0.393 606 Planarity : 0.004 0.026 579 Dihedral : 9.609 59.488 711 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.51 % Allowed : 22.57 % Favored : 71.92 % 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 0.004 0.001 ARG B 180 TYR 0.024 0.003 TYR C 158 PHE 0.018 0.003 PHE A 237 HIS 0.008 0.003 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 3516) covalent geometry : angle 0.86607 ( 4788) SS BOND : bond 0.00750 ( 3) SS BOND : angle 2.58704 ( 6) hydrogen bonds : bond 0.04007 ( 36) hydrogen bonds : angle 6.53611 ( 108) link_NAG-ASN : bond 0.01358 ( 12) link_NAG-ASN : angle 6.28654 ( 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 112 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.128 Fit side-chains REVERT: A 205 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5888 (pm20) REVERT: B 158 TYR cc_start: 0.6052 (m-80) cc_final: 0.5434 (m-10) REVERT: C 207 MET cc_start: 0.3861 (tmm) cc_final: 0.3221 (tpt) outliers start: 21 outliers final: 18 residues processed: 103 average time/residue: 0.0361 time to fit residues: 5.2736 Evaluate side-chains 96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 202 VAL 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 253 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 133 VAL 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 250 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5356 r_free = 0.5356 target = 0.280016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5564 r_free = 0.5564 target = 0.255588 restraints weight = 31309.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5523 r_free = 0.5523 target = 0.258953 restraints weight = 9582.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5530 r_free = 0.5530 target = 0.260780 restraints weight = 4787.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5528 r_free = 0.5528 target = 0.260598 restraints weight = 3864.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5530 r_free = 0.5530 target = 0.260855 restraints weight = 3334.536| |-----------------------------------------------------------------------------| r_work (final): 0.5292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5292 r_free = 0.5292 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 = 0.5292 r_free = 0.5292 target_work(ls_wunit_k1) = 0.271 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.9931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3531 Z= 0.213 Angle : 0.978 12.815 4830 Z= 0.469 Chirality : 0.062 0.391 606 Planarity : 0.003 0.020 579 Dihedral : 8.390 59.225 711 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 6.04 % Allowed : 21.52 % Favored : 72.44 % 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: -3.86 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.019 0.002 TYR C 158 PHE 0.017 0.002 PHE A 237 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 3516) covalent geometry : angle 0.82124 ( 4788) SS BOND : bond 0.00792 ( 3) SS BOND : angle 3.31711 ( 6) hydrogen bonds : bond 0.03717 ( 36) hydrogen bonds : angle 6.07258 ( 108) link_NAG-ASN : bond 0.01344 ( 12) link_NAG-ASN : angle 6.06552 ( 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 109 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.130 Fit side-chains REVERT: A 121 ILE cc_start: 0.5408 (mm) cc_final: 0.5189 (pt) REVERT: A 135 TYR cc_start: 0.5976 (m-10) cc_final: 0.4900 (p90) REVERT: A 205 GLU cc_start: 0.6496 (mm-30) cc_final: 0.5824 (pm20) REVERT: C 140 ARG cc_start: 0.4460 (OUTLIER) cc_final: 0.3331 (ptm-80) REVERT: C 207 MET cc_start: 0.3753 (tmm) cc_final: 0.2930 (tpt) REVERT: C 209 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.5885 (m-80) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.0417 time to fit residues: 5.7493 Evaluate side-chains 100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 253 CYS Chi-restraints excluded: chain B residue 133 VAL 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 171 PHE Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 209 TYR 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: 4.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5374 r_free = 0.5374 target = 0.284319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5582 r_free = 0.5582 target = 0.260407 restraints weight = 25261.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5542 r_free = 0.5542 target = 0.263631 restraints weight = 8664.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5549 r_free = 0.5549 target = 0.264767 restraints weight = 4639.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5545 r_free = 0.5545 target = 0.264743 restraints weight = 3799.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5548 r_free = 0.5548 target = 0.264962 restraints weight = 3690.654| |-----------------------------------------------------------------------------| r_work (final): 0.5311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5311 r_free = 0.5311 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 = 0.5311 r_free = 0.5311 target_work(ls_wunit_k1) = 0.275 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3531 Z= 0.169 Angle : 0.915 13.375 4830 Z= 0.434 Chirality : 0.060 0.332 606 Planarity : 0.003 0.017 579 Dihedral : 7.132 44.699 711 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.77 % Allowed : 24.15 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 180 TYR 0.011 0.002 TYR A 125 PHE 0.012 0.002 PHE A 237 HIS 0.007 0.003 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3516) covalent geometry : angle 0.75464 ( 4788) SS BOND : bond 0.00766 ( 3) SS BOND : angle 4.10125 ( 6) hydrogen bonds : bond 0.03780 ( 36) hydrogen bonds : angle 5.87329 ( 108) link_NAG-ASN : bond 0.01266 ( 12) link_NAG-ASN : angle 5.80520 ( 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 111 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.127 Fit side-chains REVERT: A 135 TYR cc_start: 0.6085 (m-10) cc_final: 0.4817 (p90) REVERT: A 205 GLU cc_start: 0.6441 (mm-30) cc_final: 0.5603 (pm20) REVERT: B 207 MET cc_start: 0.4060 (tmm) cc_final: 0.3767 (tpp) REVERT: C 140 ARG cc_start: 0.4274 (OUTLIER) cc_final: 0.3037 (ptm-80) outliers start: 22 outliers final: 18 residues processed: 104 average time/residue: 0.0407 time to fit residues: 5.7368 Evaluate side-chains 98 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 221 VAL 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 B residue 133 VAL 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 157 TYR 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 250 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5375 r_free = 0.5375 target = 0.280764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5572 r_free = 0.5572 target = 0.255453 restraints weight = 38359.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5526 r_free = 0.5526 target = 0.258921 restraints weight = 11195.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.260356 restraints weight = 5497.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5532 r_free = 0.5532 target = 0.260305 restraints weight = 4214.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.260610 restraints weight = 3970.013| |-----------------------------------------------------------------------------| r_work (final): 0.5304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5304 r_free = 0.5304 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 = 0.5304 r_free = 0.5304 target_work(ls_wunit_k1) = 0.271 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 1.0449 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= 0.195 Angle : 0.969 12.850 4830 Z= 0.461 Chirality : 0.061 0.346 606 Planarity : 0.003 0.016 579 Dihedral : 7.123 40.464 711 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 6.56 % Allowed : 24.41 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 180 TYR 0.018 0.002 TYR C 143 PHE 0.016 0.002 PHE A 237 HIS 0.008 0.003 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3516) covalent geometry : angle 0.82032 ( 4788) SS BOND : bond 0.00961 ( 3) SS BOND : angle 3.79492 ( 6) hydrogen bonds : bond 0.03926 ( 36) hydrogen bonds : angle 5.81941 ( 108) link_NAG-ASN : bond 0.01278 ( 12) link_NAG-ASN : angle 5.83950 ( 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 109 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.133 Fit side-chains REVERT: A 135 TYR cc_start: 0.6109 (m-10) cc_final: 0.4968 (p90) REVERT: A 205 GLU cc_start: 0.6582 (mm-30) cc_final: 0.5675 (pm20) REVERT: A 215 THR cc_start: 0.7252 (p) cc_final: 0.6726 (p) REVERT: C 140 ARG cc_start: 0.4291 (OUTLIER) cc_final: 0.3057 (ptm-80) REVERT: C 209 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6096 (m-80) outliers start: 25 outliers final: 19 residues processed: 100 average time/residue: 0.0435 time to fit residues: 5.8848 Evaluate side-chains 104 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 221 VAL 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 133 VAL 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 209 TYR 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: 9.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5382 r_free = 0.5382 target = 0.277736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5558 r_free = 0.5558 target = 0.252489 restraints weight = 29198.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5586 r_free = 0.5586 target = 0.255427 restraints weight = 8895.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5604 r_free = 0.5604 target = 0.257219 restraints weight = 4617.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5616 r_free = 0.5616 target = 0.258323 restraints weight = 3120.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5617 r_free = 0.5617 target = 0.258876 restraints weight = 2434.809| |-----------------------------------------------------------------------------| r_work (final): 0.5333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5333 r_free = 0.5333 target_work(ls_wunit_k1) = 0.269 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5333 r_free = 0.5333 target_work(ls_wunit_k1) = 0.269 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 1.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3531 Z= 0.235 Angle : 1.037 12.634 4830 Z= 0.501 Chirality : 0.063 0.377 606 Planarity : 0.004 0.023 579 Dihedral : 7.751 50.790 711 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.56 % Allowed : 24.15 % Favored : 69.29 % 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: -4.03 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 180 TYR 0.025 0.003 TYR C 143 PHE 0.021 0.003 PHE A 237 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 3516) covalent geometry : angle 0.89159 ( 4788) SS BOND : bond 0.01214 ( 3) SS BOND : angle 4.30976 ( 6) hydrogen bonds : bond 0.04492 ( 36) hydrogen bonds : angle 5.35929 ( 108) link_NAG-ASN : bond 0.01361 ( 12) link_NAG-ASN : angle 5.96458 ( 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 110 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.133 Fit side-chains REVERT: A 135 TYR cc_start: 0.6149 (m-10) cc_final: 0.4953 (p90) REVERT: A 192 MET cc_start: 0.7221 (mmt) cc_final: 0.6984 (mmp) REVERT: A 205 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6145 (pm20) REVERT: A 209 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5878 (m-10) REVERT: C 140 ARG cc_start: 0.3737 (OUTLIER) cc_final: 0.2598 (ptm-80) REVERT: C 209 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5482 (m-80) REVERT: C 228 MET cc_start: 0.5018 (OUTLIER) cc_final: 0.4580 (pmm) outliers start: 25 outliers final: 18 residues processed: 100 average time/residue: 0.0440 time to fit residues: 5.9428 Evaluate side-chains 103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 209 TYR Chi-restraints excluded: chain A residue 221 VAL 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 133 VAL 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 209 TYR Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5413 r_free = 0.5413 target = 0.284699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5597 r_free = 0.5597 target = 0.259884 restraints weight = 22755.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5631 r_free = 0.5631 target = 0.262915 restraints weight = 7242.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5648 r_free = 0.5648 target = 0.264641 restraints weight = 3830.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5654 r_free = 0.5654 target = 0.265718 restraints weight = 2655.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.266434 restraints weight = 2112.284| |-----------------------------------------------------------------------------| r_work (final): 0.5363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5363 r_free = 0.5363 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 = 0.5363 r_free = 0.5363 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 1.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3531 Z= 0.169 Angle : 0.943 12.982 4830 Z= 0.447 Chirality : 0.059 0.305 606 Planarity : 0.003 0.018 579 Dihedral : 6.682 39.186 711 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.25 % Allowed : 25.72 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.96 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 247 TYR 0.016 0.002 TYR C 143 PHE 0.014 0.002 PHE A 213 HIS 0.008 0.003 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3516) covalent geometry : angle 0.80870 ( 4788) SS BOND : bond 0.00875 ( 3) SS BOND : angle 2.89233 ( 6) hydrogen bonds : bond 0.03767 ( 36) hydrogen bonds : angle 5.27134 ( 108) link_NAG-ASN : bond 0.01257 ( 12) link_NAG-ASN : angle 5.56181 ( 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 107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.133 Fit side-chains REVERT: A 135 TYR cc_start: 0.6057 (m-10) cc_final: 0.4805 (p90) REVERT: A 192 MET cc_start: 0.6881 (mmt) cc_final: 0.6658 (mmp) REVERT: A 205 GLU cc_start: 0.6670 (mm-30) cc_final: 0.5779 (pm20) REVERT: A 207 MET cc_start: 0.4385 (tmm) cc_final: 0.4094 (tmm) REVERT: A 226 LEU cc_start: 0.2976 (mm) cc_final: 0.2713 (mm) REVERT: C 140 ARG cc_start: 0.4317 (OUTLIER) cc_final: 0.3066 (ptm-80) REVERT: C 206 GLU cc_start: 0.5182 (tp30) cc_final: 0.4701 (pm20) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.0409 time to fit residues: 5.4895 Evaluate side-chains 99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 172 SER Chi-restraints excluded: chain A residue 221 VAL 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 133 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.0770 chunk 33 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 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 = 0.5433 r_free = 0.5433 target = 0.285753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5581 r_free = 0.5581 target = 0.258579 restraints weight = 37875.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.262112 restraints weight = 9358.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5648 r_free = 0.5648 target = 0.264193 restraints weight = 4482.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5662 r_free = 0.5662 target = 0.265440 restraints weight = 2985.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.266062 restraints weight = 2315.797| |-----------------------------------------------------------------------------| r_work (final): 0.5368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5368 r_free = 0.5368 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 = 0.5368 r_free = 0.5368 target_work(ls_wunit_k1) = 0.277 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5725 moved from start: 1.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3531 Z= 0.192 Angle : 1.017 12.493 4830 Z= 0.486 Chirality : 0.060 0.318 606 Planarity : 0.003 0.018 579 Dihedral : 6.772 38.586 711 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.72 % Allowed : 26.77 % 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: -3.98 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 140 TYR 0.016 0.002 TYR C 143 PHE 0.038 0.004 PHE B 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3516) covalent geometry : angle 0.88595 ( 4788) SS BOND : bond 0.01116 ( 3) SS BOND : angle 4.64020 ( 6) hydrogen bonds : bond 0.04055 ( 36) hydrogen bonds : angle 5.38162 ( 108) link_NAG-ASN : bond 0.01336 ( 12) link_NAG-ASN : angle 5.55362 ( 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 105 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.151 Fit side-chains REVERT: A 135 TYR cc_start: 0.6145 (m-10) cc_final: 0.4862 (p90) REVERT: A 157 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.5252 (m-10) REVERT: A 192 MET cc_start: 0.7069 (mmt) cc_final: 0.6822 (mmp) REVERT: A 205 GLU cc_start: 0.6630 (mm-30) cc_final: 0.5860 (pm20) REVERT: A 226 LEU cc_start: 0.3193 (mm) cc_final: 0.2884 (mm) REVERT: C 140 ARG cc_start: 0.3945 (OUTLIER) cc_final: 0.2962 (ptm-80) REVERT: C 206 GLU cc_start: 0.5517 (tp30) cc_final: 0.4759 (pm20) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.0430 time to fit residues: 5.6123 Evaluate side-chains 101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 221 VAL 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 133 VAL 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 233 THR Chi-restraints excluded: chain C residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 0.0040 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5447 r_free = 0.5447 target = 0.290346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5606 r_free = 0.5606 target = 0.263497 restraints weight = 35143.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.5645 r_free = 0.5645 target = 0.267151 restraints weight = 9143.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5667 r_free = 0.5667 target = 0.269202 restraints weight = 4461.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5665 r_free = 0.5665 target = 0.270375 restraints weight = 2953.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.271206 restraints weight = 2350.722| |-----------------------------------------------------------------------------| r_work (final): 0.5388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5388 r_free = 0.5388 target_work(ls_wunit_k1) = 0.282 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5388 r_free = 0.5388 target_work(ls_wunit_k1) = 0.282 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.5388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 1.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3531 Z= 0.160 Angle : 0.968 12.824 4830 Z= 0.457 Chirality : 0.058 0.291 606 Planarity : 0.003 0.018 579 Dihedral : 6.371 37.349 711 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.67 % Allowed : 28.35 % Favored : 67.98 % 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: -3.89 (0.35), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.014 0.001 TYR C 143 PHE 0.022 0.003 PHE B 171 HIS 0.008 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3516) covalent geometry : angle 0.84106 ( 4788) SS BOND : bond 0.00689 ( 3) SS BOND : angle 3.74439 ( 6) hydrogen bonds : bond 0.03783 ( 36) hydrogen bonds : angle 5.24346 ( 108) link_NAG-ASN : bond 0.01193 ( 12) link_NAG-ASN : angle 5.40237 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 894.58 seconds wall clock time: 16 minutes 4.35 seconds (964.35 seconds total)