Starting phenix.real_space_refine on Sat Aug 23 09:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sar_24954/08_2025/7sar_24954.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 70 5.16 5 C 7260 2.51 5 N 1770 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11420 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, F, G, H, I, J Time building chain proxies: 1.49, per 1000 atoms: 0.13 Number of scatterers: 11420 At special positions: 0 Unit cell: (177.1, 218.9, 42.9, 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 70 16.00 O 2320 8.00 N 1770 7.00 C 7260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, 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 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 214 " - pdb=" SG CYS H 253 " distance=2.03 Simple disulfide: pdb=" SG CYS I 214 " - pdb=" SG CYS I 253 " distance=2.03 Simple disulfide: pdb=" SG CYS J 214 " - pdb=" SG CYS J 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 151 " " NAG A 302 " - " ASN A 164 " " NAG A 303 " - " ASN A 183 " " NAG A 304 " - " ASN A 145 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 164 " " NAG B 303 " - " ASN B 183 " " NAG B 304 " - " ASN B 145 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 164 " " NAG C 303 " - " ASN C 183 " " NAG C 304 " - " ASN C 145 " " NAG D 301 " - " ASN D 151 " " NAG D 302 " - " ASN D 164 " " NAG D 303 " - " ASN D 183 " " NAG D 304 " - " ASN D 145 " " NAG E 301 " - " ASN E 151 " " NAG E 302 " - " ASN E 164 " " NAG E 303 " - " ASN E 183 " " NAG E 304 " - " ASN E 145 " " NAG F 301 " - " ASN F 151 " " NAG F 302 " - " ASN F 164 " " NAG F 303 " - " ASN F 183 " " NAG F 304 " - " ASN F 145 " " NAG G 301 " - " ASN G 151 " " NAG G 302 " - " ASN G 164 " " NAG G 303 " - " ASN G 183 " " NAG G 304 " - " ASN G 145 " " NAG H 301 " - " ASN H 151 " " NAG H 302 " - " ASN H 164 " " NAG H 303 " - " ASN H 183 " " NAG H 304 " - " ASN H 145 " " NAG I 301 " - " ASN I 151 " " NAG I 302 " - " ASN I 164 " " NAG I 303 " - " ASN I 183 " " NAG I 304 " - " ASN I 145 " " NAG J 301 " - " ASN J 151 " " NAG J 302 " - " ASN J 164 " " NAG J 303 " - " ASN J 183 " " NAG J 304 " - " ASN J 145 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 417.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 72.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 122 through 126 removed outlier: 6.630A pdb=" N VAL D 123 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE G 126 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR D 125 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 123 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR A 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 129 through 138 removed outlier: 9.043A pdb=" N SER D 130 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N VAL G 133 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR D 132 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TYR G 135 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER D 134 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL G 137 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP D 136 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N SER A 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N VAL D 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR A 132 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR D 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N SER A 134 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL D 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP A 136 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER F 130 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA A 131 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR F 132 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER I 130 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA F 131 " --> pdb=" O SER I 130 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR I 132 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 142 through 143 removed outlier: 6.289A pdb=" N ILE D 142 " --> pdb=" O TYR G 143 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 146 through 160 removed outlier: 6.744A pdb=" N ILE A 146 " --> pdb=" O THR F 147 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR F 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN A 148 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN F 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 150 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR F 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 152 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN F 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 154 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N TYR F 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN A 156 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER F 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 158 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 146 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR I 149 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN F 148 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASN I 151 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU F 150 " --> pdb=" O ASN I 151 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR I 153 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 152 " --> pdb=" O THR I 153 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASN I 155 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN F 154 " --> pdb=" O ASN I 155 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TYR I 157 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN F 156 " --> pdb=" O TYR I 157 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER I 159 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR F 158 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 163 through 177 removed outlier: 5.787A pdb=" N ASN D 164 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA G 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR D 166 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL G 169 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN D 168 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N PHE G 171 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N GLN D 170 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N LYS G 173 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N SER D 172 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N VAL G 175 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N THR D 174 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N GLY G 177 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N ILE D 176 " --> pdb=" O GLY G 177 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN A 164 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA D 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR A 166 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N VAL D 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLN A 168 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N PHE D 171 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N GLN A 170 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N LYS D 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N SER A 172 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL D 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N THR A 174 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N GLY D 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE A 176 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 167 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLN F 168 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 169 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN F 170 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 171 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER F 172 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A 173 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR F 174 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 175 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 176 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY A 177 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA F 167 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN I 168 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL F 169 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLN I 170 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE F 171 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER I 172 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS F 173 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR I 174 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 175 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE I 176 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY F 177 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 180 through 187 removed outlier: 7.015A pdb=" N ILE D 184 " --> pdb=" O ASN G 183 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR G 185 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE D 186 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE G 187 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 184 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR D 185 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 186 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 187 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 181 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE F 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 183 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N ILE F 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N THR A 185 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU F 181 " --> pdb=" O ASN I 182 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE I 184 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN F 183 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N ILE I 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR F 185 " --> pdb=" O ILE I 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 194 through 198 removed outlier: 6.719A pdb=" N ILE A 195 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR F 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 197 " --> pdb=" O THR F 198 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE F 195 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR I 198 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR F 197 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 201 through 205 removed outlier: 6.400A pdb=" N VAL D 202 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU G 205 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 204 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 202 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLU D 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A 204 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 209 through 230 removed outlier: 7.113A pdb=" N MET D 210 " --> pdb=" O TYR G 209 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR G 211 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP D 212 " --> pdb=" O TYR G 211 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE G 213 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N CYS D 214 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS D 220 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL G 221 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS D 222 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN G 223 " --> pdb=" O HIS D 222 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLN G 229 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 230 " --> pdb=" O GLN G 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N MET A 210 " --> pdb=" O TYR D 209 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR D 211 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP A 212 " --> pdb=" O TYR D 211 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE D 213 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS A 214 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS A 220 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 221 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N HIS A 222 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN D 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN D 229 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 230 " --> pdb=" O GLN D 229 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N TYR A 209 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N ASP F 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N TYR A 211 " --> pdb=" O ASP F 212 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N CYS F 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE A 213 " --> pdb=" O CYS F 214 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N LEU F 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 215 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N SER F 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 217 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LYS F 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILE A 219 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N HIS F 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N VAL A 221 " --> pdb=" O HIS F 222 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ILE F 224 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN A 223 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU F 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 225 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET F 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N MET A 227 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL F 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLN A 229 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N TYR F 209 " --> pdb=" O MET I 210 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N ASP I 212 " --> pdb=" O TYR F 209 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N TYR F 211 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N CYS I 214 " --> pdb=" O TYR F 211 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE F 213 " --> pdb=" O CYS I 214 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LEU I 216 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR F 215 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N SER I 218 " --> pdb=" O THR F 215 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE F 217 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS I 220 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE F 219 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N HIS I 222 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N VAL F 221 " --> pdb=" O HIS I 222 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N ILE I 224 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN F 223 " --> pdb=" O ILE I 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU I 226 " --> pdb=" O ASN F 223 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL F 225 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET I 228 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N MET F 227 " --> pdb=" O MET I 228 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL I 230 " --> pdb=" O MET F 227 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN F 229 " --> pdb=" O VAL I 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 233 through 253 removed outlier: 7.055A pdb=" N VAL G 251 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP D 252 " --> pdb=" O VAL G 251 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS G 253 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ASP A 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS D 253 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A 233 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR F 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 235 " --> pdb=" O TYR F 236 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY F 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 237 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER F 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A 239 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLN F 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU A 241 " --> pdb=" O GLN F 242 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N SER F 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 243 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLU F 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 245 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR F 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG A 247 " --> pdb=" O TYR F 248 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR F 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N GLN A 249 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASP F 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N VAL A 251 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR F 233 " --> pdb=" O THR I 234 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR I 236 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR F 235 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY I 238 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE F 237 " --> pdb=" O GLY I 238 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER I 240 " --> pdb=" O PHE F 237 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS F 239 " --> pdb=" O SER I 240 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLN I 242 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU F 241 " --> pdb=" O GLN I 242 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N SER I 244 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE F 243 " --> pdb=" O SER I 244 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLU I 246 " --> pdb=" O ILE F 243 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN F 245 " --> pdb=" O GLU I 246 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR I 248 " --> pdb=" O GLN F 245 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG F 247 " --> pdb=" O TYR I 248 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR I 250 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLN F 249 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP I 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N VAL F 251 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 122 through 126 removed outlier: 6.608A pdb=" N VAL C 123 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE H 126 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR C 125 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 129 through 138 removed outlier: 9.063A pdb=" N SER C 130 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N VAL H 133 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C 132 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYR H 135 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N SER C 134 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL H 137 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP C 136 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N SER B 130 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N VAL C 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR B 132 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR C 135 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER E 130 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA B 131 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR E 132 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER J 130 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA E 131 " --> pdb=" O SER J 130 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR J 132 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 142 through 143 removed outlier: 6.329A pdb=" N ILE C 142 " --> pdb=" O TYR H 143 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 160 removed outlier: 6.731A pdb=" N ILE B 146 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR E 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN B 148 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASN E 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 150 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR E 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 152 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ASN E 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 154 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TYR E 157 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN B 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER E 159 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR B 158 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE E 146 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N THR J 149 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN E 148 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASN J 151 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU E 150 " --> pdb=" O ASN J 151 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N THR J 153 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE E 152 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN J 155 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN E 154 " --> pdb=" O ASN J 155 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR J 157 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN E 156 " --> pdb=" O TYR J 157 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER J 159 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR E 158 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 163 through 177 removed outlier: 5.801A pdb=" N ASN C 164 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA H 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR C 166 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL H 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N GLN C 168 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N PHE H 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N GLN C 170 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N LYS H 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N SER C 172 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N VAL H 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N THR C 174 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N GLY H 177 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ILE C 176 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN B 164 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA C 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR B 166 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL C 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N PHE C 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N GLN B 170 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N LYS C 173 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N SER B 172 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N VAL C 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N THR B 174 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 10.613A pdb=" N GLY C 177 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ILE B 176 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA B 167 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN E 168 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 169 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN E 170 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE B 171 " --> pdb=" O GLN E 170 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER E 172 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS B 173 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR E 174 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 175 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 176 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY B 177 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA E 167 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN J 168 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL E 169 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLN J 170 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE E 171 " --> pdb=" O GLN J 170 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER J 172 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS E 173 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR J 174 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 175 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE J 176 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY E 177 " --> pdb=" O ILE J 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 180 through 187 removed outlier: 7.016A pdb=" N ILE C 184 " --> pdb=" O ASN H 183 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR H 185 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 186 " --> pdb=" O THR H 185 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE H 187 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 184 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C 185 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE B 186 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 187 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 181 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE E 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN B 183 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N ILE E 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N THR B 185 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 181 " --> pdb=" O ASN J 182 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE J 184 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASN E 183 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N ILE J 186 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N THR E 185 " --> pdb=" O ILE J 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 194 through 198 removed outlier: 6.719A pdb=" N ILE B 195 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR B 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE E 195 " --> pdb=" O ASP J 196 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR J 198 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR E 197 " --> pdb=" O THR J 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 201 through 205 removed outlier: 6.395A pdb=" N VAL C 202 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLU H 205 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 204 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU C 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 204 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 209 through 230 removed outlier: 7.113A pdb=" N MET C 210 " --> pdb=" O TYR H 209 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR H 211 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASP C 212 " --> pdb=" O TYR H 211 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE H 213 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS C 214 " --> pdb=" O PHE H 213 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS C 220 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL H 221 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS C 222 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN H 223 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLN H 229 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 230 " --> pdb=" O GLN H 229 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET B 210 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR C 211 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 212 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE C 213 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS B 214 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS B 220 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 221 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS B 222 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN C 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLN C 229 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 230 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N TYR B 209 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N ASP E 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N TYR B 211 " --> pdb=" O ASP E 212 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N CYS E 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE B 213 " --> pdb=" O CYS E 214 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LEU E 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 215 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N SER E 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 217 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS E 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 219 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N HIS E 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N VAL B 221 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N ILE E 224 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN B 223 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU E 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 225 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N MET E 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N MET B 227 " --> pdb=" O MET E 228 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL E 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLN B 229 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N TYR E 209 " --> pdb=" O MET J 210 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N ASP J 212 " --> pdb=" O TYR E 209 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N TYR E 211 " --> pdb=" O ASP J 212 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N CYS J 214 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N PHE E 213 " --> pdb=" O CYS J 214 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LEU J 216 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR E 215 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N SER J 218 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE E 217 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LYS J 220 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ILE E 219 " --> pdb=" O LYS J 220 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N HIS J 222 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N VAL E 221 " --> pdb=" O HIS J 222 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE J 224 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASN E 223 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU J 226 " --> pdb=" O ASN E 223 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL E 225 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET J 228 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N MET E 227 " --> pdb=" O MET J 228 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL J 230 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLN E 229 " --> pdb=" O VAL J 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 233 through 253 removed outlier: 7.055A pdb=" N VAL H 251 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP C 252 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N CYS H 253 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP B 252 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 253 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR B 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR E 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR B 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLY E 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SER E 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS B 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLN E 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU B 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER E 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLU E 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR E 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG B 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR E 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLN B 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP E 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N VAL B 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR E 233 " --> pdb=" O THR J 234 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR J 236 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR E 235 " --> pdb=" O TYR J 236 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLY J 238 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE E 237 " --> pdb=" O GLY J 238 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER J 240 " --> pdb=" O PHE E 237 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS E 239 " --> pdb=" O SER J 240 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLN J 242 " --> pdb=" O HIS E 239 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU E 241 " --> pdb=" O GLN J 242 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER J 244 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 243 " --> pdb=" O SER J 244 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLU J 246 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN E 245 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR J 248 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG E 247 " --> pdb=" O TYR J 248 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR J 250 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N GLN E 249 " --> pdb=" O TYR J 250 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP J 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 251 " --> pdb=" O ASP J 252 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 792 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: 1.96 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3500 1.34 - 1.46: 2619 1.46 - 1.58: 5361 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 11600 Sorted by residual: bond pdb=" N VAL J 123 " pdb=" CA VAL J 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.07e+00 bond pdb=" N VAL H 123 " pdb=" CA VAL H 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 8.99e+00 bond pdb=" N VAL G 123 " pdb=" CA VAL G 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 8.99e+00 bond pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 8.96e+00 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 8.96e+00 ... (remaining 11595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 14287 1.30 - 2.59: 1211 2.59 - 3.89: 237 3.89 - 5.18: 15 5.18 - 6.48: 20 Bond angle restraints: 15770 Sorted by residual: angle pdb=" CA ILE G 121 " pdb=" C ILE G 121 " pdb=" O ILE G 121 " ideal model delta sigma weight residual 121.17 117.54 3.63 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA ILE B 121 " pdb=" C ILE B 121 " pdb=" O ILE B 121 " ideal model delta sigma weight residual 121.17 117.55 3.62 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA ILE A 121 " pdb=" C ILE A 121 " pdb=" O ILE A 121 " ideal model delta sigma weight residual 121.17 117.56 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" CA ILE F 121 " pdb=" C ILE F 121 " pdb=" O ILE F 121 " ideal model delta sigma weight residual 121.17 117.56 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" CA ILE E 121 " pdb=" C ILE E 121 " pdb=" O ILE E 121 " ideal model delta sigma weight residual 121.17 117.56 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 15765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 6720 15.68 - 31.36: 560 31.36 - 47.04: 120 47.04 - 62.73: 70 62.73 - 78.41: 20 Dihedral angle restraints: 7490 sinusoidal: 3430 harmonic: 4060 Sorted by residual: dihedral pdb=" CA GLU A 246 " pdb=" C GLU A 246 " pdb=" N ARG A 247 " pdb=" CA ARG A 247 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU F 246 " pdb=" C GLU F 246 " pdb=" N ARG F 247 " pdb=" CA ARG F 247 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLU J 246 " pdb=" C GLU J 246 " pdb=" N ARG J 247 " pdb=" CA ARG J 247 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1595 0.075 - 0.151: 375 0.151 - 0.226: 20 0.226 - 0.302: 0 0.302 - 0.377: 20 Chirality restraints: 2010 Sorted by residual: 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 -2.02 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C1 NAG A 302 " pdb=" ND2 ASN A 164 " pdb=" C2 NAG A 302 " pdb=" O5 NAG A 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C1 NAG F 302 " pdb=" ND2 ASN F 164 " pdb=" C2 NAG F 302 " pdb=" O5 NAG F 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 2007 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN H 138 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLN H 138 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN H 138 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS H 139 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 138 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C GLN E 138 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN E 138 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS E 139 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 138 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C GLN B 138 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN B 138 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 139 " 0.019 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 190 2.71 - 3.25: 10330 3.25 - 3.80: 17659 3.80 - 4.35: 22341 4.35 - 4.90: 35758 Nonbonded interactions: 86278 Sorted by model distance: nonbonded pdb=" OG1 THR B 231 " pdb=" OG1 THR B 234 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR J 231 " pdb=" OG1 THR J 234 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR H 231 " pdb=" OG1 THR H 234 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR E 231 " pdb=" OG1 THR E 234 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C 231 " pdb=" OG1 THR C 234 " model vdw 2.157 3.040 ... (remaining 86273 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.160 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.005 0.041 11650 Z= 0.274 Angle : 0.875 9.682 15910 Z= 0.464 Chirality : 0.067 0.377 2010 Planarity : 0.006 0.033 1900 Dihedral : 13.629 78.407 4860 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 aren not related in a simple way. whole: -3.51 (0.18), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 180 TYR 0.012 0.001 TYR C 209 PHE 0.039 0.006 PHE D 171 HIS 0.003 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00515 (11600) covalent geometry : angle 0.79507 (15770) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.44301 ( 20) hydrogen bonds : bond 0.16903 ( 264) hydrogen bonds : angle 10.83930 ( 792) link_NAG-ASN : bond 0.00443 ( 40) link_NAG-ASN : angle 4.27903 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.429 Fit side-chains REVERT: G 210 MET cc_start: 0.6487 (ttt) cc_final: 0.6093 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0957 time to fit residues: 18.8797 Evaluate side-chains 111 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 156 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 ASN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 ASN J 239 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.139463 restraints weight = 13039.222| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.91 r_work: 0.4282 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11650 Z= 0.169 Angle : 0.756 11.705 15910 Z= 0.393 Chirality : 0.060 0.419 2010 Planarity : 0.003 0.018 1900 Dihedral : 9.021 58.736 2330 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.83 % Allowed : 8.97 % Favored : 89.21 % 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 aren not related in a simple way. whole: -2.71 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 140 TYR 0.020 0.002 TYR B 143 PHE 0.031 0.003 PHE E 171 HIS 0.005 0.001 HIS H 239 Details of bonding type rmsd covalent geometry : bond 0.00401 (11600) covalent geometry : angle 0.67360 (15770) SS BOND : bond 0.00193 ( 10) SS BOND : angle 0.76230 ( 20) hydrogen bonds : bond 0.03526 ( 264) hydrogen bonds : angle 6.30031 ( 792) link_NAG-ASN : bond 0.00362 ( 40) link_NAG-ASN : angle 3.99468 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.411 Fit side-chains REVERT: A 152 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 249 GLN cc_start: 0.7942 (tt0) cc_final: 0.7136 (mt0) REVERT: D 207 MET cc_start: 0.7149 (mtt) cc_final: 0.6869 (mtp) REVERT: E 207 MET cc_start: 0.6399 (mtt) cc_final: 0.6096 (mpp) REVERT: G 180 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7182 (mtp180) REVERT: I 180 ARG cc_start: 0.7222 (mtt180) cc_final: 0.5844 (mmp-170) REVERT: I 196 ASP cc_start: 0.8145 (m-30) cc_final: 0.7944 (m-30) REVERT: I 207 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: J 173 LYS cc_start: 0.7951 (tttt) cc_final: 0.7717 (ttmt) outliers start: 23 outliers final: 10 residues processed: 143 average time/residue: 0.1032 time to fit residues: 21.2086 Evaluate side-chains 126 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 163 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 239 HIS B 249 GLN C 239 HIS D 239 HIS F 239 HIS G 156 ASN G 239 HIS G 242 GLN H 239 HIS I 239 HIS ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.159357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.133646 restraints weight = 13524.652| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.86 r_work: 0.4224 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11650 Z= 0.206 Angle : 0.782 11.779 15910 Z= 0.407 Chirality : 0.061 0.420 2010 Planarity : 0.003 0.023 1900 Dihedral : 8.311 55.387 2330 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.49 % Allowed : 12.86 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.21), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 140 TYR 0.025 0.002 TYR J 143 PHE 0.030 0.003 PHE A 171 HIS 0.006 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00498 (11600) covalent geometry : angle 0.69885 (15770) SS BOND : bond 0.00225 ( 10) SS BOND : angle 0.67547 ( 20) hydrogen bonds : bond 0.03697 ( 264) hydrogen bonds : angle 5.78715 ( 792) link_NAG-ASN : bond 0.00304 ( 40) link_NAG-ASN : angle 4.09210 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.425 Fit side-chains REVERT: A 138 GLN cc_start: 0.6756 (tt0) cc_final: 0.6522 (mp10) REVERT: A 152 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 249 GLN cc_start: 0.7832 (tt0) cc_final: 0.7057 (mt0) REVERT: D 207 MET cc_start: 0.7219 (mtt) cc_final: 0.6937 (mtp) REVERT: E 138 GLN cc_start: 0.6897 (tt0) cc_final: 0.6481 (mp10) REVERT: E 207 MET cc_start: 0.6799 (mtt) cc_final: 0.6448 (mpp) REVERT: G 138 GLN cc_start: 0.7431 (mp10) cc_final: 0.6972 (tt0) REVERT: I 180 ARG cc_start: 0.7067 (mtt180) cc_final: 0.5698 (mmp-170) REVERT: J 161 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7625 (mm-30) outliers start: 44 outliers final: 38 residues processed: 147 average time/residue: 0.1017 time to fit residues: 21.7100 Evaluate side-chains 158 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN E 239 HIS F 138 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** 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 = 0.4542 r_free = 0.4542 target = 0.151940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.127347 restraints weight = 14036.386| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.81 r_work: 0.4151 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 11650 Z= 0.332 Angle : 0.928 14.475 15910 Z= 0.479 Chirality : 0.065 0.432 2010 Planarity : 0.004 0.028 1900 Dihedral : 9.079 55.151 2330 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.95 % Allowed : 13.10 % Favored : 80.95 % 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 aren not related in a simple way. whole: -2.93 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 140 TYR 0.029 0.003 TYR A 209 PHE 0.035 0.004 PHE A 171 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00788 (11600) covalent geometry : angle 0.83316 (15770) SS BOND : bond 0.00174 ( 10) SS BOND : angle 0.81767 ( 20) hydrogen bonds : bond 0.04587 ( 264) hydrogen bonds : angle 5.72137 ( 792) link_NAG-ASN : bond 0.00289 ( 40) link_NAG-ASN : angle 4.77902 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7829 (mt) REVERT: A 171 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7506 (t80) REVERT: A 249 GLN cc_start: 0.8042 (tt0) cc_final: 0.7212 (mt0) REVERT: E 138 GLN cc_start: 0.7217 (tt0) cc_final: 0.6800 (mp10) REVERT: E 207 MET cc_start: 0.7040 (mtt) cc_final: 0.6816 (mtm) REVERT: E 249 GLN cc_start: 0.8008 (tt0) cc_final: 0.7250 (mt0) REVERT: G 138 GLN cc_start: 0.7685 (mp10) cc_final: 0.7292 (tt0) REVERT: G 180 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7386 (mtt90) REVERT: H 246 GLU cc_start: 0.8669 (pt0) cc_final: 0.8345 (pt0) REVERT: I 180 ARG cc_start: 0.7130 (mtt180) cc_final: 0.6028 (mmp-170) REVERT: J 161 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7862 (mm-30) REVERT: J 175 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8293 (m) REVERT: J 249 GLN cc_start: 0.7807 (tt0) cc_final: 0.7479 (mt0) outliers start: 75 outliers final: 55 residues processed: 186 average time/residue: 0.0916 time to fit residues: 24.9524 Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain D residue 152 ILE 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 216 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 GLN D 138 GLN F 182 ASN I 182 ASN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.124006 restraints weight = 13934.676| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.86 r_work: 0.4149 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11650 Z= 0.171 Angle : 0.750 12.584 15910 Z= 0.385 Chirality : 0.061 0.412 2010 Planarity : 0.003 0.023 1900 Dihedral : 8.078 51.026 2330 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.19 % Allowed : 14.52 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 140 TYR 0.017 0.002 TYR A 209 PHE 0.026 0.003 PHE A 171 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00408 (11600) covalent geometry : angle 0.65995 (15770) SS BOND : bond 0.00123 ( 10) SS BOND : angle 0.52229 ( 20) hydrogen bonds : bond 0.03297 ( 264) hydrogen bonds : angle 5.53369 ( 792) link_NAG-ASN : bond 0.00385 ( 40) link_NAG-ASN : angle 4.15879 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7735 (mt) REVERT: A 249 GLN cc_start: 0.7972 (tt0) cc_final: 0.7209 (mt0) REVERT: B 161 GLU cc_start: 0.8493 (mp0) cc_final: 0.8278 (mp0) REVERT: D 207 MET cc_start: 0.7338 (mtt) cc_final: 0.6983 (mtp) REVERT: E 138 GLN cc_start: 0.7086 (tt0) cc_final: 0.6637 (mp10) REVERT: E 196 ASP cc_start: 0.8214 (m-30) cc_final: 0.7907 (m-30) REVERT: G 138 GLN cc_start: 0.7679 (mp10) cc_final: 0.7294 (tt0) REVERT: G 143 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5158 (m-80) REVERT: J 161 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7871 (mm-30) REVERT: J 175 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8205 (m) outliers start: 78 outliers final: 65 residues processed: 189 average time/residue: 0.0932 time to fit residues: 26.1705 Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 131 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 152 ILE 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 F residue 141 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 0.0870 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 61 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 2.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.156140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.129451 restraints weight = 13572.671| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.91 r_work: 0.4216 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11650 Z= 0.100 Angle : 0.652 10.939 15910 Z= 0.335 Chirality : 0.059 0.387 2010 Planarity : 0.003 0.022 1900 Dihedral : 7.285 47.031 2330 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.52 % Allowed : 16.27 % Favored : 79.21 % 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 aren not related in a simple way. whole: -2.84 (0.21), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 140 TYR 0.012 0.001 TYR J 143 PHE 0.021 0.002 PHE D 171 HIS 0.003 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00226 (11600) covalent geometry : angle 0.57194 (15770) SS BOND : bond 0.00144 ( 10) SS BOND : angle 0.30963 ( 20) hydrogen bonds : bond 0.02443 ( 264) hydrogen bonds : angle 5.27170 ( 792) link_NAG-ASN : bond 0.00548 ( 40) link_NAG-ASN : angle 3.64406 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.7417 (mp10) cc_final: 0.7185 (mp10) REVERT: A 152 ILE cc_start: 0.8061 (tt) cc_final: 0.7690 (mt) REVERT: A 210 MET cc_start: 0.7601 (ttt) cc_final: 0.7342 (tpp) REVERT: A 228 MET cc_start: 0.8661 (tpp) cc_final: 0.8209 (tpp) REVERT: A 249 GLN cc_start: 0.7891 (tt0) cc_final: 0.7122 (mt0) REVERT: B 207 MET cc_start: 0.7704 (mtp) cc_final: 0.7187 (mtm) REVERT: B 228 MET cc_start: 0.8912 (tpp) cc_final: 0.8614 (tpp) REVERT: D 207 MET cc_start: 0.7354 (mtt) cc_final: 0.6465 (mtp) REVERT: E 138 GLN cc_start: 0.7003 (tt0) cc_final: 0.6559 (mp10) REVERT: E 196 ASP cc_start: 0.8218 (m-30) cc_final: 0.7912 (m-30) REVERT: F 150 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7527 (tt) REVERT: F 152 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7970 (mt) REVERT: G 138 GLN cc_start: 0.7619 (mp10) cc_final: 0.7196 (tt0) REVERT: G 210 MET cc_start: 0.7557 (ttt) cc_final: 0.7345 (tpp) REVERT: G 228 MET cc_start: 0.7751 (ttp) cc_final: 0.7500 (tpp) REVERT: H 216 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8120 (pp) REVERT: H 228 MET cc_start: 0.8619 (tpp) cc_final: 0.8413 (tpp) REVERT: I 180 ARG cc_start: 0.6919 (mtt180) cc_final: 0.5679 (mmp-170) REVERT: I 246 GLU cc_start: 0.8477 (pt0) cc_final: 0.8275 (pt0) REVERT: J 161 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7835 (mm-30) REVERT: J 175 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8209 (m) REVERT: J 192 MET cc_start: 0.7891 (mmt) cc_final: 0.7603 (mmt) outliers start: 57 outliers final: 40 residues processed: 175 average time/residue: 0.1003 time to fit residues: 25.3279 Evaluate side-chains 179 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 40.0000 chunk 59 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN D 182 ASN J 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.146113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.120440 restraints weight = 14139.706| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.86 r_work: 0.4094 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 11650 Z= 0.266 Angle : 0.839 13.325 15910 Z= 0.431 Chirality : 0.064 0.454 2010 Planarity : 0.003 0.026 1900 Dihedral : 8.433 53.249 2330 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 5.95 % Allowed : 15.63 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 140 TYR 0.023 0.003 TYR E 143 PHE 0.028 0.003 PHE A 171 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00638 (11600) covalent geometry : angle 0.74977 (15770) SS BOND : bond 0.00127 ( 10) SS BOND : angle 0.68665 ( 20) hydrogen bonds : bond 0.04002 ( 264) hydrogen bonds : angle 5.44762 ( 792) link_NAG-ASN : bond 0.00377 ( 40) link_NAG-ASN : angle 4.40392 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 145 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 210 MET cc_start: 0.7860 (ttt) cc_final: 0.7647 (tpp) REVERT: A 249 GLN cc_start: 0.8219 (tt0) cc_final: 0.7384 (mt0) REVERT: E 138 GLN cc_start: 0.7132 (tt0) cc_final: 0.6736 (mp10) REVERT: E 249 GLN cc_start: 0.8142 (tt0) cc_final: 0.7364 (mt0) REVERT: F 150 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7890 (tt) REVERT: F 152 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8056 (mt) REVERT: G 143 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5013 (m-80) REVERT: H 246 GLU cc_start: 0.8691 (pt0) cc_final: 0.8451 (pt0) REVERT: J 175 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (m) REVERT: J 249 GLN cc_start: 0.8126 (tt0) cc_final: 0.7654 (mt0) outliers start: 75 outliers final: 61 residues processed: 196 average time/residue: 0.1009 time to fit residues: 28.5056 Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 152 ILE 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 F residue 141 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 143 TYR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 218 SER Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 208 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 175 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0753 > 50: distance: 9 - 147: 34.142 distance: 49 - 184: 34.075 distance: 52 - 197: 24.337 distance: 64 - 200: 31.002 distance: 67 - 212: 21.184 distance: 79 - 215: 35.079 distance: 143 - 147: 31.650 distance: 147 - 148: 45.931 distance: 148 - 149: 48.393 distance: 148 - 151: 37.158 distance: 149 - 150: 11.177 distance: 149 - 155: 26.863 distance: 151 - 152: 34.636 distance: 151 - 153: 4.976 distance: 152 - 154: 44.959 distance: 155 - 156: 11.111 distance: 156 - 157: 41.870 distance: 156 - 159: 44.790 distance: 157 - 158: 34.393 distance: 157 - 164: 26.938 distance: 159 - 160: 29.003 distance: 160 - 161: 21.888 distance: 161 - 162: 16.840 distance: 162 - 163: 24.078 distance: 164 - 165: 16.865 distance: 165 - 166: 43.582 distance: 166 - 167: 42.396 distance: 168 - 170: 56.300 distance: 172 - 173: 54.310 distance: 172 - 175: 3.068 distance: 173 - 174: 10.914 distance: 173 - 181: 44.871 distance: 175 - 176: 23.294 distance: 176 - 177: 5.394 distance: 176 - 178: 42.689 distance: 177 - 179: 38.165 distance: 178 - 180: 15.073 distance: 179 - 180: 41.780 distance: 181 - 182: 38.984 distance: 182 - 183: 30.073 distance: 182 - 185: 45.156 distance: 183 - 184: 11.271 distance: 183 - 189: 24.425 distance: 186 - 187: 52.066 distance: 186 - 188: 55.897 distance: 189 - 190: 22.939 distance: 190 - 191: 50.388 distance: 190 - 193: 36.471 distance: 191 - 197: 45.951 distance: 193 - 194: 3.350 distance: 193 - 195: 20.141 distance: 194 - 196: 27.491 distance: 197 - 198: 41.046 distance: 198 - 199: 33.035 distance: 198 - 201: 4.475 distance: 199 - 200: 3.248 distance: 199 - 204: 32.202 distance: 201 - 202: 37.200 distance: 201 - 203: 11.974 distance: 205 - 206: 12.150 distance: 205 - 208: 42.035 distance: 206 - 207: 48.079 distance: 206 - 212: 24.348 distance: 208 - 209: 44.975 distance: 209 - 210: 50.937 distance: 209 - 211: 8.157 distance: 212 - 213: 13.780 distance: 213 - 214: 26.017 distance: 213 - 216: 3.187 distance: 214 - 220: 27.664 distance: 216 - 217: 7.680 distance: 217 - 218: 25.515 distance: 218 - 219: 26.451 distance: 220 - 221: 11.990 distance: 221 - 222: 27.711 distance: 221 - 224: 41.972 distance: 222 - 223: 49.525 distance: 222 - 228: 26.729 distance: 224 - 225: 23.962 distance: 225 - 226: 12.484 distance: 226 - 227: 43.476