Starting phenix.real_space_refine on Tue Mar 3 13:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7saq_24953/03_2026/7saq_24953.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 35 5.16 5 C 3630 2.51 5 N 885 2.21 5 O 1160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 5710 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} 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 Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.77, per 1000 atoms: 0.13 Number of scatterers: 5710 At special positions: 0 Unit cell: (106.7, 122.1, 45.1, 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 35 16.00 O 1160 8.00 N 885 7.00 C 3630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 145 " " NAG A 302 " - " ASN A 164 " " NAG A 303 " - " ASN A 183 " " NAG A 304 " - " ASN A 151 " " NAG B 301 " - " ASN B 145 " " NAG B 302 " - " ASN B 164 " " NAG B 303 " - " ASN B 183 " " NAG B 304 " - " ASN B 151 " " NAG C 301 " - " ASN C 145 " " NAG C 302 " - " ASN C 164 " " NAG C 303 " - " ASN C 183 " " NAG C 304 " - " ASN C 151 " " NAG D 301 " - " ASN D 145 " " NAG D 302 " - " ASN D 164 " " NAG D 303 " - " ASN D 183 " " NAG D 304 " - " ASN D 151 " " NAG E 301 " - " ASN E 145 " " NAG E 302 " - " ASN E 164 " " NAG E 303 " - " ASN E 183 " " NAG E 304 " - " ASN E 151 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 328.0 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1300 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 74.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 122 through 126 removed outlier: 6.689A pdb=" N VAL A 123 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE D 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR A 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 138 removed outlier: 7.067A pdb=" N SER C 130 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 131 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR C 132 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N SER D 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA C 131 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR D 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N SER A 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N VAL D 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 132 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR D 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER A 134 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL D 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP A 136 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER E 130 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 131 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR E 132 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 143 removed outlier: 6.578A pdb=" N ILE A 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 177 removed outlier: 6.549A pdb=" N ILE B 146 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR C 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 148 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN C 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 150 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR C 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 152 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASN C 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 154 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR C 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN B 156 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER C 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 158 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU C 161 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL B 160 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU C 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N VAL B 162 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ILE C 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N ALA C 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR B 166 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL C 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE C 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS C 173 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER B 172 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL C 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 174 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY C 177 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 176 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 146 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR D 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN C 148 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN D 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU C 150 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR D 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE C 152 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN D 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 154 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR D 157 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 156 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER D 159 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR C 158 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU D 161 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL C 160 " --> pdb=" O GLU D 161 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU D 163 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N VAL C 162 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ILE D 165 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ASN C 164 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ALA D 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 166 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL D 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN C 168 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE D 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN C 170 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LYS D 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER C 172 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL D 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 174 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY D 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 176 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D 162 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU A 163 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN D 164 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 165 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR D 166 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 146 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR E 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 148 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ASN E 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 150 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR E 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 152 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN E 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 154 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR E 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER E 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR A 158 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLU E 161 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL A 160 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL A 162 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE E 165 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N ASN A 164 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N ALA E 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR A 166 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL E 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 168 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE E 171 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN A 170 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS E 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 172 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL E 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 174 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLY E 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 176 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 180 through 187 removed outlier: 6.140A pdb=" N LEU B 181 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASN B 183 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N ILE C 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THR B 185 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU C 181 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 184 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASN C 183 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N ILE D 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N THR C 185 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 184 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR D 185 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 186 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE D 187 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 181 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE E 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN A 183 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 10.143A pdb=" N ILE E 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N THR A 185 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 198 removed outlier: 6.616A pdb=" N ILE B 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR C 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 195 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR D 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR C 197 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 195 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR E 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 205 removed outlier: 6.404A pdb=" N VAL A 202 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU D 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 204 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 230 removed outlier: 6.989A pdb=" N THR C 215 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 216 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 217 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER B 218 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 219 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 224 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 225 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 226 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET C 227 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET B 228 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR D 215 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU C 216 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE D 217 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER C 218 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE D 219 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 224 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 225 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU C 226 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET D 227 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET C 228 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR A 209 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP D 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 211 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS D 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N PHE A 213 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU D 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR A 215 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N SER D 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ILE A 217 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N LYS D 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE A 219 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS D 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 221 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN A 223 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N LEU D 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N VAL A 225 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N MET D 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET A 227 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N VAL D 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN A 229 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 215 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 216 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE E 217 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER A 218 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE E 219 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE A 224 " --> pdb=" O ASN E 223 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL E 225 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 226 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET E 227 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET A 228 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 233 through 253 removed outlier: 6.692A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 233 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR D 236 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 235 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 237 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER D 240 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS C 239 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLN D 242 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 241 " --> pdb=" O GLN D 242 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER D 244 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 243 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLU D 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN C 245 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N TYR D 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG C 247 " --> pdb=" O TYR D 248 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR D 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLN C 249 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP D 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N VAL C 251 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL D 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP A 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS D 253 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR E 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY E 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER E 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLN E 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER E 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLU E 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR E 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N TYR E 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLN A 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASP E 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N VAL A 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 384 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: 0.87 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1749 1.34 - 1.46: 1093 1.46 - 1.58: 2898 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 5800 Sorted by residual: bond pdb=" N VAL E 123 " pdb=" CA VAL E 123 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.11e+00 bond pdb=" N VAL D 123 " pdb=" CA VAL D 123 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.86e+00 bond pdb=" N VAL C 123 " pdb=" CA VAL C 123 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.19e-02 7.06e+03 8.86e+00 bond pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 5795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 6755 1.07 - 2.14: 816 2.14 - 3.22: 240 3.22 - 4.29: 69 4.29 - 5.36: 5 Bond angle restraints: 7885 Sorted by residual: angle pdb=" CA ILE D 121 " pdb=" C ILE D 121 " pdb=" O ILE D 121 " ideal model delta sigma weight residual 121.17 117.47 3.70 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA ILE E 121 " pdb=" C ILE E 121 " pdb=" O ILE E 121 " ideal model delta sigma weight residual 121.17 117.49 3.68 1.06e+00 8.90e-01 1.20e+01 angle pdb=" CA ILE B 121 " pdb=" C ILE B 121 " pdb=" O ILE B 121 " ideal model delta sigma weight residual 121.17 117.50 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" CA ILE A 121 " pdb=" C ILE A 121 " pdb=" O ILE A 121 " ideal model delta sigma weight residual 121.17 117.51 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA ILE C 121 " pdb=" C ILE C 121 " pdb=" O ILE C 121 " ideal model delta sigma weight residual 121.17 117.55 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 7880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3391 17.07 - 34.14: 257 34.14 - 51.21: 57 51.21 - 68.28: 30 68.28 - 85.36: 10 Dihedral angle restraints: 3745 sinusoidal: 1715 harmonic: 2030 Sorted by residual: dihedral pdb=" CA GLU B 246 " pdb=" C GLU B 246 " pdb=" N ARG B 247 " pdb=" CA ARG B 247 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU C 246 " pdb=" C GLU C 246 " pdb=" N ARG C 247 " pdb=" CA ARG C 247 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLU E 246 " pdb=" C GLU E 246 " pdb=" N ARG E 247 " pdb=" CA ARG E 247 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 3742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 720 0.060 - 0.121: 243 0.121 - 0.181: 27 0.181 - 0.241: 0 0.241 - 0.301: 15 Chirality restraints: 1005 Sorted by residual: chirality pdb=" C1 NAG C 302 " pdb=" ND2 ASN C 164 " pdb=" C2 NAG C 302 " pdb=" O5 NAG C 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG D 302 " pdb=" ND2 ASN D 164 " pdb=" C2 NAG D 302 " pdb=" O5 NAG D 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG E 302 " pdb=" ND2 ASN E 164 " pdb=" C2 NAG E 302 " pdb=" O5 NAG E 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1002 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG B 302 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG D 302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG D 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG D 302 " 0.187 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 302 " 0.324 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C7 NAG A 302 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 302 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 302 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG A 302 " 0.187 2.00e-02 2.50e+03 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 548 2.77 - 3.30: 5087 3.30 - 3.84: 9748 3.84 - 4.37: 10559 4.37 - 4.90: 17198 Nonbonded interactions: 43140 Sorted by model distance: nonbonded pdb=" OG1 THR E 231 " pdb=" OG1 THR E 234 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 231 " pdb=" OG1 THR A 234 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR D 231 " pdb=" OG1 THR D 234 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 231 " pdb=" OG1 THR B 234 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.241 3.040 ... (remaining 43135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5825 Z= 0.302 Angle : 1.007 14.162 7955 Z= 0.525 Chirality : 0.065 0.301 1005 Planarity : 0.022 0.281 950 Dihedral : 14.709 85.356 2430 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: -3.19 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.104 0.005 TYR A 125 PHE 0.010 0.002 PHE E 213 HIS 0.002 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 5800) covalent geometry : angle 0.83909 ( 7885) SS BOND : bond 0.00102 ( 5) SS BOND : angle 0.41643 ( 10) hydrogen bonds : bond 0.14588 ( 128) hydrogen bonds : angle 11.23135 ( 384) link_NAG-ASN : bond 0.01919 ( 20) link_NAG-ASN : angle 6.48148 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.7455 (ttm) cc_final: 0.7185 (ttm) REVERT: C 228 MET cc_start: 0.7396 (ttm) cc_final: 0.7195 (ttm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.6659 time to fit residues: 42.8855 Evaluate side-chains 53 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 249 GLN B 154 ASN B 249 GLN C 154 ASN C 156 ASN C 249 GLN D 154 ASN D 249 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.156949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.127377 restraints weight = 5921.567| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.71 r_work: 0.4226 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5825 Z= 0.190 Angle : 0.842 12.739 7955 Z= 0.429 Chirality : 0.062 0.468 1005 Planarity : 0.003 0.024 950 Dihedral : 8.510 45.486 1165 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.59 % Allowed : 10.63 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.29), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 247 TYR 0.029 0.002 TYR D 125 PHE 0.008 0.001 PHE C 213 HIS 0.006 0.002 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5800) covalent geometry : angle 0.74049 ( 7885) SS BOND : bond 0.00462 ( 5) SS BOND : angle 0.16887 ( 10) hydrogen bonds : bond 0.03538 ( 128) hydrogen bonds : angle 6.76089 ( 384) link_NAG-ASN : bond 0.00187 ( 20) link_NAG-ASN : angle 4.67442 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: C 207 MET cc_start: 0.6067 (tmt) cc_final: 0.5658 (ttm) REVERT: D 207 MET cc_start: 0.6344 (tmm) cc_final: 0.5821 (ttp) outliers start: 10 outliers final: 3 residues processed: 73 average time/residue: 0.6422 time to fit residues: 48.7541 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain D residue 174 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN B 138 GLN B 182 ASN C 138 GLN C 168 GLN C 182 ASN D 182 ASN E 156 ASN E 182 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.148823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.120179 restraints weight = 6019.543| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.62 r_work: 0.4152 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5825 Z= 0.276 Angle : 0.921 15.170 7955 Z= 0.474 Chirality : 0.068 0.609 1005 Planarity : 0.003 0.020 950 Dihedral : 7.484 33.785 1165 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.17 % Allowed : 15.40 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.28), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.022 0.003 TYR E 135 PHE 0.011 0.002 PHE B 213 HIS 0.012 0.004 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 5800) covalent geometry : angle 0.81577 ( 7885) SS BOND : bond 0.00586 ( 5) SS BOND : angle 0.40625 ( 10) hydrogen bonds : bond 0.04083 ( 128) hydrogen bonds : angle 6.16750 ( 384) link_NAG-ASN : bond 0.00405 ( 20) link_NAG-ASN : angle 5.00456 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.243 Fit side-chains REVERT: A 138 GLN cc_start: 0.7244 (tt0) cc_final: 0.6964 (tt0) REVERT: B 207 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6218 (ttm) REVERT: C 124 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8112 (mmmm) REVERT: C 138 GLN cc_start: 0.7650 (tt0) cc_final: 0.7312 (tt0) REVERT: C 175 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 207 MET cc_start: 0.6293 (tmt) cc_final: 0.5944 (mtp) REVERT: D 207 MET cc_start: 0.6410 (tmm) cc_final: 0.6167 (ttp) REVERT: E 207 MET cc_start: 0.6527 (tmm) cc_final: 0.6140 (mpt) outliers start: 20 outliers final: 8 residues processed: 79 average time/residue: 0.6022 time to fit residues: 49.6105 Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.144605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.117307 restraints weight = 6331.893| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.54 r_work: 0.4151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5825 Z= 0.194 Angle : 0.826 14.245 7955 Z= 0.418 Chirality : 0.065 0.576 1005 Planarity : 0.003 0.019 950 Dihedral : 6.960 31.796 1165 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.018 0.002 TYR C 143 PHE 0.011 0.002 PHE C 213 HIS 0.009 0.003 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5800) covalent geometry : angle 0.71521 ( 7885) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.26004 ( 10) hydrogen bonds : bond 0.03300 ( 128) hydrogen bonds : angle 5.84555 ( 384) link_NAG-ASN : bond 0.00503 ( 20) link_NAG-ASN : angle 4.79519 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7293 (tt0) cc_final: 0.6994 (tt0) REVERT: B 124 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7521 (mttp) REVERT: B 175 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8211 (t) REVERT: B 192 MET cc_start: 0.8171 (tpp) cc_final: 0.7254 (mmm) REVERT: B 207 MET cc_start: 0.6634 (tmm) cc_final: 0.6278 (ttm) REVERT: C 124 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8203 (mmmm) REVERT: C 138 GLN cc_start: 0.7743 (tt0) cc_final: 0.7389 (tt0) REVERT: C 207 MET cc_start: 0.6394 (tmt) cc_final: 0.5938 (mtp) REVERT: D 207 MET cc_start: 0.6411 (tmm) cc_final: 0.6193 (ttp) REVERT: E 228 MET cc_start: 0.8487 (ttm) cc_final: 0.8218 (tpp) REVERT: E 247 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8422 (ttt180) outliers start: 21 outliers final: 13 residues processed: 79 average time/residue: 0.6092 time to fit residues: 50.1325 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.121576 restraints weight = 6115.588| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.61 r_work: 0.4165 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5825 Z= 0.235 Angle : 0.868 14.023 7955 Z= 0.442 Chirality : 0.067 0.664 1005 Planarity : 0.003 0.020 950 Dihedral : 7.061 32.167 1165 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.44 % Allowed : 17.62 % Favored : 77.94 % 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: -3.08 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.020 0.003 TYR E 135 PHE 0.010 0.002 PHE C 213 HIS 0.011 0.003 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 5800) covalent geometry : angle 0.76127 ( 7885) SS BOND : bond 0.00427 ( 5) SS BOND : angle 1.65553 ( 10) hydrogen bonds : bond 0.03685 ( 128) hydrogen bonds : angle 5.82279 ( 384) link_NAG-ASN : bond 0.00450 ( 20) link_NAG-ASN : angle 4.81912 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.222 Fit side-chains REVERT: A 138 GLN cc_start: 0.7307 (tt0) cc_final: 0.6952 (tt0) REVERT: A 192 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6784 (mmt) REVERT: B 124 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7462 (mttp) REVERT: B 175 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (t) REVERT: B 192 MET cc_start: 0.8236 (tpp) cc_final: 0.7360 (mmm) REVERT: C 124 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8122 (mmmm) REVERT: C 138 GLN cc_start: 0.7561 (tt0) cc_final: 0.7159 (tt0) REVERT: C 175 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7574 (t) REVERT: C 207 MET cc_start: 0.6360 (tmt) cc_final: 0.5825 (mtp) REVERT: D 175 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7547 (t) REVERT: E 178 LYS cc_start: 0.7618 (mttp) cc_final: 0.7232 (ttmm) REVERT: E 207 MET cc_start: 0.6559 (tmm) cc_final: 0.6115 (mpt) REVERT: E 247 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8480 (ttt180) outliers start: 28 outliers final: 15 residues processed: 83 average time/residue: 0.6077 time to fit residues: 52.4257 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.150584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.122452 restraints weight = 6056.786| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.53 r_work: 0.4192 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5825 Z= 0.217 Angle : 0.846 13.968 7955 Z= 0.429 Chirality : 0.066 0.599 1005 Planarity : 0.003 0.019 950 Dihedral : 6.872 32.543 1165 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.13 % Allowed : 19.05 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.019 0.003 TYR E 135 PHE 0.010 0.002 PHE C 213 HIS 0.009 0.003 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 5800) covalent geometry : angle 0.73877 ( 7885) SS BOND : bond 0.00364 ( 5) SS BOND : angle 1.63472 ( 10) hydrogen bonds : bond 0.03448 ( 128) hydrogen bonds : angle 5.74340 ( 384) link_NAG-ASN : bond 0.00462 ( 20) link_NAG-ASN : angle 4.76893 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7369 (tt0) cc_final: 0.6904 (tt0) REVERT: A 192 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6742 (mmt) REVERT: B 124 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7462 (mttp) REVERT: B 175 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 192 MET cc_start: 0.8164 (tpp) cc_final: 0.7209 (mmm) REVERT: B 207 MET cc_start: 0.6656 (tmm) cc_final: 0.6341 (mtm) REVERT: C 124 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8131 (mmmm) REVERT: C 138 GLN cc_start: 0.7564 (tt0) cc_final: 0.7095 (tt0) REVERT: C 175 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7556 (t) REVERT: C 207 MET cc_start: 0.6378 (tmt) cc_final: 0.5770 (mtp) REVERT: D 175 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7536 (t) REVERT: D 178 LYS cc_start: 0.7398 (ttmm) cc_final: 0.6970 (ttpp) REVERT: E 178 LYS cc_start: 0.7640 (mttp) cc_final: 0.7229 (ttmm) REVERT: E 207 MET cc_start: 0.6584 (tmm) cc_final: 0.6044 (mpt) REVERT: E 247 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8434 (ttt180) outliers start: 26 outliers final: 17 residues processed: 83 average time/residue: 0.6223 time to fit residues: 53.7923 Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.146921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.118708 restraints weight = 6214.599| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.63 r_work: 0.4147 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 5825 Z= 0.285 Angle : 0.927 14.951 7955 Z= 0.472 Chirality : 0.071 0.755 1005 Planarity : 0.003 0.021 950 Dihedral : 7.233 33.848 1165 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.97 % Allowed : 19.84 % Favored : 76.19 % 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 (0.26), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 180 TYR 0.022 0.003 TYR E 135 PHE 0.011 0.002 PHE B 213 HIS 0.010 0.003 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00668 ( 5800) covalent geometry : angle 0.81788 ( 7885) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.93423 ( 10) hydrogen bonds : bond 0.04100 ( 128) hydrogen bonds : angle 5.82521 ( 384) link_NAG-ASN : bond 0.00517 ( 20) link_NAG-ASN : angle 5.03418 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7443 (tt0) cc_final: 0.6967 (tt0) REVERT: A 192 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6914 (mmt) REVERT: B 124 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7464 (mttp) REVERT: B 175 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8202 (t) REVERT: B 181 LEU cc_start: 0.8577 (mp) cc_final: 0.8230 (mt) REVERT: B 192 MET cc_start: 0.8492 (tpp) cc_final: 0.7405 (mmm) REVERT: B 207 MET cc_start: 0.6722 (tmm) cc_final: 0.6398 (mtm) REVERT: C 124 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8153 (mmmm) REVERT: C 138 GLN cc_start: 0.7560 (tt0) cc_final: 0.7048 (tt0) REVERT: C 207 MET cc_start: 0.6442 (tmt) cc_final: 0.5833 (mtp) REVERT: D 178 LYS cc_start: 0.7489 (ttmm) cc_final: 0.7151 (ttpp) REVERT: E 178 LYS cc_start: 0.7746 (mttp) cc_final: 0.7229 (ttmm) REVERT: E 192 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7597 (mtp) REVERT: E 247 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8457 (ttt180) outliers start: 25 outliers final: 19 residues processed: 82 average time/residue: 0.6204 time to fit residues: 52.9189 Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 249 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.142937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.116040 restraints weight = 6449.838| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.53 r_work: 0.4148 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5825 Z= 0.210 Angle : 0.851 13.961 7955 Z= 0.430 Chirality : 0.067 0.641 1005 Planarity : 0.003 0.021 950 Dihedral : 6.845 33.565 1165 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.29 % Allowed : 19.68 % Favored : 76.03 % 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: -3.33 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.019 0.002 TYR E 248 PHE 0.010 0.002 PHE A 213 HIS 0.009 0.003 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 5800) covalent geometry : angle 0.74141 ( 7885) SS BOND : bond 0.00377 ( 5) SS BOND : angle 1.29048 ( 10) hydrogen bonds : bond 0.03401 ( 128) hydrogen bonds : angle 5.71199 ( 384) link_NAG-ASN : bond 0.00524 ( 20) link_NAG-ASN : angle 4.85918 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7588 (tt0) cc_final: 0.7112 (tt0) REVERT: A 192 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6875 (mmt) REVERT: A 210 MET cc_start: 0.7581 (ttm) cc_final: 0.7263 (ttm) REVERT: B 124 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7561 (mttp) REVERT: B 175 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8266 (t) REVERT: B 192 MET cc_start: 0.8310 (tpp) cc_final: 0.7391 (mmm) REVERT: B 207 MET cc_start: 0.6717 (tmm) cc_final: 0.6426 (mtm) REVERT: C 124 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8183 (mmmm) REVERT: C 138 GLN cc_start: 0.7749 (tt0) cc_final: 0.7238 (tt0) REVERT: C 175 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7718 (t) REVERT: C 207 MET cc_start: 0.6548 (tmt) cc_final: 0.5954 (mtp) REVERT: D 175 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7642 (t) REVERT: D 178 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7332 (ttpp) REVERT: D 192 MET cc_start: 0.8015 (mpp) cc_final: 0.7539 (mmm) REVERT: E 178 LYS cc_start: 0.7845 (mttp) cc_final: 0.7383 (ttmm) REVERT: E 192 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7531 (mtp) REVERT: E 207 MET cc_start: 0.6741 (tmm) cc_final: 0.6200 (mpt) REVERT: E 247 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (ttt180) outliers start: 27 outliers final: 18 residues processed: 81 average time/residue: 0.6277 time to fit residues: 52.8476 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.144788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.117834 restraints weight = 6383.790| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 2.47 r_work: 0.4166 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5825 Z= 0.181 Angle : 0.817 13.371 7955 Z= 0.411 Chirality : 0.065 0.594 1005 Planarity : 0.003 0.021 950 Dihedral : 6.614 33.515 1165 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.33 % Allowed : 21.11 % Favored : 75.56 % 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: -3.29 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.018 0.002 TYR E 248 PHE 0.009 0.002 PHE C 213 HIS 0.009 0.003 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5800) covalent geometry : angle 0.70860 ( 7885) SS BOND : bond 0.00295 ( 5) SS BOND : angle 1.13291 ( 10) hydrogen bonds : bond 0.03126 ( 128) hydrogen bonds : angle 5.63010 ( 384) link_NAG-ASN : bond 0.00517 ( 20) link_NAG-ASN : angle 4.71579 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7517 (tt0) cc_final: 0.7029 (tt0) REVERT: A 192 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6817 (mmt) REVERT: A 210 MET cc_start: 0.7571 (ttm) cc_final: 0.7251 (ttm) REVERT: B 124 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7522 (mttp) REVERT: B 192 MET cc_start: 0.8251 (tpp) cc_final: 0.7353 (mmm) REVERT: B 207 MET cc_start: 0.6693 (tmm) cc_final: 0.6392 (mtm) REVERT: C 124 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8215 (mmmm) REVERT: C 138 GLN cc_start: 0.7784 (tt0) cc_final: 0.7285 (tt0) REVERT: C 175 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7749 (t) REVERT: C 207 MET cc_start: 0.6543 (tmt) cc_final: 0.5949 (mtp) REVERT: D 175 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7657 (t) REVERT: D 178 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7394 (ttpp) REVERT: D 192 MET cc_start: 0.7995 (mpp) cc_final: 0.7527 (mmm) REVERT: E 178 LYS cc_start: 0.7823 (mttp) cc_final: 0.7384 (ttmm) REVERT: E 241 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: E 247 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8329 (ttt180) outliers start: 21 outliers final: 13 residues processed: 76 average time/residue: 0.6385 time to fit residues: 50.3766 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 48 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 156 ASN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.148409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.120461 restraints weight = 6249.143| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.53 r_work: 0.4164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4037 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 5825 Z= 0.284 Angle : 0.930 15.164 7955 Z= 0.474 Chirality : 0.070 0.660 1005 Planarity : 0.003 0.025 950 Dihedral : 7.122 33.621 1165 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.97 % Allowed : 20.63 % Favored : 75.40 % 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: -3.35 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 140 TYR 0.023 0.003 TYR E 248 PHE 0.011 0.002 PHE A 213 HIS 0.009 0.003 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 5800) covalent geometry : angle 0.82581 ( 7885) SS BOND : bond 0.00518 ( 5) SS BOND : angle 1.57063 ( 10) hydrogen bonds : bond 0.04055 ( 128) hydrogen bonds : angle 5.80733 ( 384) link_NAG-ASN : bond 0.00473 ( 20) link_NAG-ASN : angle 4.95658 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7426 (tt0) cc_final: 0.6945 (tt0) REVERT: A 178 LYS cc_start: 0.7021 (mttp) cc_final: 0.6483 (ttmm) REVERT: A 192 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6863 (mmt) REVERT: A 210 MET cc_start: 0.7571 (ttm) cc_final: 0.7235 (ttm) REVERT: B 124 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7457 (mttp) REVERT: B 175 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8235 (t) REVERT: B 181 LEU cc_start: 0.8577 (mp) cc_final: 0.8255 (mt) REVERT: B 192 MET cc_start: 0.8491 (tpp) cc_final: 0.7429 (mmm) REVERT: B 207 MET cc_start: 0.6671 (tmm) cc_final: 0.6347 (mtm) REVERT: C 124 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8133 (mmmm) REVERT: C 138 GLN cc_start: 0.7595 (tt0) cc_final: 0.7071 (tt0) REVERT: C 207 MET cc_start: 0.6424 (tmt) cc_final: 0.5834 (mtp) REVERT: D 178 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7237 (ttpp) REVERT: E 178 LYS cc_start: 0.7720 (mttp) cc_final: 0.7273 (ttmm) REVERT: E 207 MET cc_start: 0.6594 (tmm) cc_final: 0.6083 (mpt) REVERT: E 247 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8434 (ttt180) outliers start: 25 outliers final: 19 residues processed: 82 average time/residue: 0.6565 time to fit residues: 55.9775 Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 168 GLN E 239 HIS E 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.148185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.120144 restraints weight = 6168.180| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.52 r_work: 0.4177 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5825 Z= 0.273 Angle : 0.929 14.853 7955 Z= 0.473 Chirality : 0.071 0.725 1005 Planarity : 0.003 0.025 950 Dihedral : 7.290 37.378 1165 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.97 % Allowed : 21.90 % Favored : 74.13 % 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: -3.36 (0.27), residues: 665 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 180 TYR 0.022 0.003 TYR E 248 PHE 0.010 0.002 PHE A 213 HIS 0.009 0.003 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 5800) covalent geometry : angle 0.82258 ( 7885) SS BOND : bond 0.00505 ( 5) SS BOND : angle 1.48274 ( 10) hydrogen bonds : bond 0.03943 ( 128) hydrogen bonds : angle 5.76869 ( 384) link_NAG-ASN : bond 0.00542 ( 20) link_NAG-ASN : angle 5.01284 ( 60) =============================================================================== Job complete usr+sys time: 1948.39 seconds wall clock time: 33 minutes 59.49 seconds (2039.49 seconds total)