Starting phenix.real_space_refine on Tue Jul 29 06:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sar_24954/07_2025/7sar_24954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sar_24954/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sar_24954/07_2025/7sar_24954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sar_24954/07_2025/7sar_24954.map" model { file = "/net/cci-nas-00/data/ceres_data/7sar_24954/07_2025/7sar_24954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sar_24954/07_2025/7sar_24954.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.41, per 1000 atoms: 0.30 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 C 214 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS I 214 " - pdb=" SG CYS I 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 214 " - pdb=" SG CYS H 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.23 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: 2.76 Time building geometry restraints manager: 3.59 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS F 239 PHE 0.039 0.006 PHE D 171 TYR 0.012 0.001 TYR C 209 ARG 0.001 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 40) link_NAG-ASN : angle 4.27903 ( 120) hydrogen bonds : bond 0.16903 ( 264) hydrogen bonds : angle 10.83930 ( 792) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.44301 ( 20) covalent geometry : bond 0.00515 (11600) covalent geometry : angle 0.79507 (15770) *********************** 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 : 1.282 Fit side-chains REVERT: G 210 MET cc_start: 0.6487 (ttt) cc_final: 0.6096 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2207 time to fit residues: 43.2929 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 : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** G 156 ASN H 156 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.162472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.136054 restraints weight = 13162.413| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.88 r_work: 0.4252 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11650 Z= 0.205 Angle : 0.801 12.324 15910 Z= 0.417 Chirality : 0.062 0.428 2010 Planarity : 0.003 0.022 1900 Dihedral : 9.305 59.551 2330 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.14 % Allowed : 9.60 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 239 PHE 0.033 0.003 PHE E 171 TYR 0.022 0.002 TYR B 143 ARG 0.003 0.001 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 40) link_NAG-ASN : angle 4.22453 ( 120) hydrogen bonds : bond 0.03978 ( 264) hydrogen bonds : angle 6.34845 ( 792) SS BOND : bond 0.00219 ( 10) SS BOND : angle 0.83886 ( 20) covalent geometry : bond 0.00487 (11600) covalent geometry : angle 0.71493 (15770) *********************** 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 157 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.225 Fit side-chains REVERT: A 249 GLN cc_start: 0.7976 (tt0) cc_final: 0.7154 (mt0) REVERT: D 207 MET cc_start: 0.7301 (mtt) cc_final: 0.6988 (mtp) REVERT: G 180 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7215 (mtp180) REVERT: I 180 ARG cc_start: 0.7257 (mtt180) cc_final: 0.5836 (mmp-170) REVERT: J 173 LYS cc_start: 0.7996 (tttt) cc_final: 0.7731 (ttmt) outliers start: 27 outliers final: 15 residues processed: 143 average time/residue: 0.2306 time to fit residues: 47.6944 Evaluate side-chains 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 163 GLU 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 216 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 230 VAL 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 26 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 24 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- 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 E 239 HIS F 239 HIS G 239 HIS ** I 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 HIS ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.156215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.131022 restraints weight = 13733.651| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.82 r_work: 0.4184 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11650 Z= 0.254 Angle : 0.846 12.940 15910 Z= 0.439 Chirality : 0.063 0.433 2010 Planarity : 0.004 0.025 1900 Dihedral : 8.768 59.777 2330 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.97 % Allowed : 12.94 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 239 PHE 0.035 0.003 PHE A 171 TYR 0.026 0.003 TYR J 143 ARG 0.004 0.001 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 40) link_NAG-ASN : angle 4.42302 ( 120) hydrogen bonds : bond 0.04106 ( 264) hydrogen bonds : angle 5.81188 ( 792) SS BOND : bond 0.00200 ( 10) SS BOND : angle 0.77402 ( 20) covalent geometry : bond 0.00609 (11600) covalent geometry : angle 0.75711 (15770) *********************** 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 178 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 138 GLN cc_start: 0.6992 (tt0) cc_final: 0.6671 (mp10) REVERT: A 152 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 249 GLN cc_start: 0.7839 (tt0) cc_final: 0.7074 (mt0) REVERT: D 207 MET cc_start: 0.7279 (mtt) cc_final: 0.6946 (mtp) REVERT: E 138 GLN cc_start: 0.7032 (tt0) cc_final: 0.6539 (mp10) REVERT: G 138 GLN cc_start: 0.7419 (mp10) cc_final: 0.7127 (pm20) REVERT: I 180 ARG cc_start: 0.7089 (mtt180) cc_final: 0.5684 (mmp-170) REVERT: J 161 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7661 (mm-30) REVERT: J 175 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8244 (m) outliers start: 50 outliers final: 42 residues processed: 156 average time/residue: 0.2266 time to fit residues: 51.0805 Evaluate side-chains 166 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 152 ILE 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 G residue 230 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 112 optimal weight: 0.0170 chunk 126 optimal weight: 20.0000 overall best weight: 5.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.152666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.126177 restraints weight = 13717.878| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.88 r_work: 0.4171 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11650 Z= 0.150 Angle : 0.712 11.567 15910 Z= 0.368 Chirality : 0.059 0.408 2010 Planarity : 0.003 0.017 1900 Dihedral : 7.869 57.850 2330 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.40 % Allowed : 13.10 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 239 PHE 0.023 0.002 PHE A 171 TYR 0.016 0.002 TYR J 143 ARG 0.002 0.000 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 40) link_NAG-ASN : angle 3.96072 ( 120) hydrogen bonds : bond 0.03129 ( 264) hydrogen bonds : angle 5.50915 ( 792) SS BOND : bond 0.00138 ( 10) SS BOND : angle 0.49142 ( 20) covalent geometry : bond 0.00355 (11600) covalent geometry : angle 0.62577 (15770) *********************** 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 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 127 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLN cc_start: 0.6913 (tt0) cc_final: 0.6711 (mp10) REVERT: A 152 ILE cc_start: 0.8140 (tt) cc_final: 0.7789 (mt) REVERT: A 249 GLN cc_start: 0.7911 (tt0) cc_final: 0.7143 (mt0) REVERT: D 207 MET cc_start: 0.7323 (mtt) cc_final: 0.6620 (mtp) REVERT: E 138 GLN cc_start: 0.6963 (tt0) cc_final: 0.6505 (mp10) REVERT: E 196 ASP cc_start: 0.8224 (m-30) cc_final: 0.7920 (m-30) REVERT: J 161 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 68 outliers final: 55 residues processed: 167 average time/residue: 0.2017 time to fit residues: 49.9191 Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 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 163 GLU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 175 VAL 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 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 141 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 H residue 152 ILE Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 174 THR 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 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 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 1 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.147193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.121525 restraints weight = 14011.054| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.84 r_work: 0.4099 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.006 0.062 11650 Z= 0.271 Angle : 0.847 13.488 15910 Z= 0.437 Chirality : 0.063 0.416 2010 Planarity : 0.004 0.024 1900 Dihedral : 8.648 58.846 2330 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 6.19 % Allowed : 14.21 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 239 PHE 0.027 0.003 PHE A 171 TYR 0.025 0.003 TYR A 209 ARG 0.003 0.001 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 40) link_NAG-ASN : angle 4.47194 ( 120) hydrogen bonds : bond 0.04118 ( 264) hydrogen bonds : angle 5.55950 ( 792) SS BOND : bond 0.00126 ( 10) SS BOND : angle 0.71363 ( 20) covalent geometry : bond 0.00647 (11600) covalent geometry : angle 0.75601 (15770) *********************** 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 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 137 time to evaluate : 1.391 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: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 249 GLN cc_start: 0.8167 (tt0) cc_final: 0.7308 (mt0) REVERT: D 207 MET cc_start: 0.7455 (mtt) cc_final: 0.7205 (mtp) REVERT: E 138 GLN cc_start: 0.7141 (tt0) cc_final: 0.6663 (mp10) REVERT: J 175 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8236 (m) REVERT: J 249 GLN cc_start: 0.7934 (tt0) cc_final: 0.7568 (mt0) outliers start: 78 outliers final: 67 residues processed: 187 average time/residue: 0.2265 time to fit residues: 62.4006 Evaluate side-chains 200 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 131 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 174 THR 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 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 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 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 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 141 THR 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 H residue 145 ASN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 230 VAL 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 141 THR 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 93 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 182 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 ASN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.148770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.122829 restraints weight = 14145.562| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.86 r_work: 0.4122 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11650 Z= 0.198 Angle : 0.778 12.739 15910 Z= 0.398 Chirality : 0.062 0.410 2010 Planarity : 0.003 0.024 1900 Dihedral : 8.345 58.984 2330 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 6.67 % Allowed : 15.71 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 239 PHE 0.022 0.003 PHE A 171 TYR 0.019 0.002 TYR A 209 ARG 0.003 0.000 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 40) link_NAG-ASN : angle 4.27714 ( 120) hydrogen bonds : bond 0.03503 ( 264) hydrogen bonds : angle 5.46683 ( 792) SS BOND : bond 0.00120 ( 10) SS BOND : angle 0.57620 ( 20) covalent geometry : bond 0.00471 (11600) covalent geometry : angle 0.68607 (15770) *********************** 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 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 1.282 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: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 228 MET cc_start: 0.8624 (tpp) cc_final: 0.8250 (tpp) REVERT: A 249 GLN cc_start: 0.8004 (tt0) cc_final: 0.7311 (mt0) REVERT: D 207 MET cc_start: 0.7344 (mtt) cc_final: 0.6586 (mtp) REVERT: E 138 GLN cc_start: 0.7115 (tt0) cc_final: 0.6710 (mp10) REVERT: E 196 ASP cc_start: 0.8219 (m-30) cc_final: 0.7906 (m-30) REVERT: G 138 GLN cc_start: 0.7529 (mp10) cc_final: 0.7099 (mt0) REVERT: G 143 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.5149 (m-80) REVERT: J 175 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8230 (m) REVERT: J 249 GLN cc_start: 0.7949 (tt0) cc_final: 0.7494 (mt0) outliers start: 84 outliers final: 71 residues processed: 195 average time/residue: 0.2088 time to fit residues: 60.1315 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 134 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 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 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 C residue 218 SER 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 174 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 208 SER 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 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 H residue 141 THR Chi-restraints excluded: chain H residue 145 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 82 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 9 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4564 r_free = 0.4564 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.127221 restraints weight = 13769.259| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.90 r_work: 0.4184 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11650 Z= 0.117 Angle : 0.688 11.292 15910 Z= 0.352 Chirality : 0.061 0.475 2010 Planarity : 0.003 0.029 1900 Dihedral : 7.570 54.328 2330 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 5.24 % Allowed : 16.83 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 239 PHE 0.019 0.002 PHE D 171 TYR 0.018 0.001 TYR A 143 ARG 0.002 0.000 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 40) link_NAG-ASN : angle 3.85449 ( 120) hydrogen bonds : bond 0.02649 ( 264) hydrogen bonds : angle 5.33543 ( 792) SS BOND : bond 0.00139 ( 10) SS BOND : angle 0.36838 ( 20) covalent geometry : bond 0.00273 (11600) covalent geometry : angle 0.60400 (15770) *********************** 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 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 140 time to evaluate : 1.183 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 138 GLN cc_start: 0.7207 (mp10) cc_final: 0.6588 (mt0) REVERT: A 152 ILE cc_start: 0.8121 (tt) cc_final: 0.7807 (mt) REVERT: A 175 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7621 (p) REVERT: A 228 MET cc_start: 0.8643 (tpp) cc_final: 0.8222 (tpp) REVERT: A 249 GLN cc_start: 0.7938 (tt0) cc_final: 0.7172 (mt0) REVERT: D 207 MET cc_start: 0.7320 (mtt) cc_final: 0.6538 (mtp) REVERT: E 138 GLN cc_start: 0.7092 (tt0) cc_final: 0.6664 (mp10) REVERT: E 196 ASP cc_start: 0.8148 (m-30) cc_final: 0.7859 (m-30) REVERT: F 150 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7664 (tt) REVERT: F 152 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8000 (mt) REVERT: G 138 GLN cc_start: 0.7533 (mp10) cc_final: 0.6963 (pm20) REVERT: G 143 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: H 216 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8133 (pp) REVERT: I 180 ARG cc_start: 0.6944 (mtt180) cc_final: 0.5678 (mmp-170) outliers start: 66 outliers final: 48 residues processed: 185 average time/residue: 0.2064 time to fit residues: 56.0631 Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL 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 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 141 THR 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 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 174 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain F residue 141 THR 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 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 208 SER Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 216 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 20.0000 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4514 r_free = 0.4514 target = 0.149203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.123064 restraints weight = 13871.314| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 2.88 r_work: 0.4139 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11650 Z= 0.176 Angle : 0.753 12.105 15910 Z= 0.386 Chirality : 0.062 0.482 2010 Planarity : 0.003 0.029 1900 Dihedral : 7.776 54.262 2330 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 5.71 % Allowed : 16.75 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 239 PHE 0.020 0.003 PHE E 171 TYR 0.021 0.002 TYR A 143 ARG 0.002 0.000 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 40) link_NAG-ASN : angle 4.11645 ( 120) hydrogen bonds : bond 0.03234 ( 264) hydrogen bonds : angle 5.35944 ( 792) SS BOND : bond 0.00132 ( 10) SS BOND : angle 0.51396 ( 20) covalent geometry : bond 0.00422 (11600) covalent geometry : angle 0.66517 (15770) *********************** REFINEMENT MACRO_CYCLE 8 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 211 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 1.288 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: symmetry clash REVERT: A 138 GLN cc_start: 0.7215 (mp10) cc_final: 0.6859 (mt0) REVERT: A 152 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7833 (mt) REVERT: A 228 MET cc_start: 0.8696 (tpp) cc_final: 0.8329 (tpp) REVERT: A 249 GLN cc_start: 0.8027 (tt0) cc_final: 0.7215 (mt0) REVERT: B 228 MET cc_start: 0.8901 (tpp) cc_final: 0.8677 (tpp) REVERT: D 207 MET cc_start: 0.7439 (mtt) cc_final: 0.7121 (mtp) REVERT: E 138 GLN cc_start: 0.7108 (tt0) cc_final: 0.6705 (mp10) REVERT: E 196 ASP cc_start: 0.8151 (m-30) cc_final: 0.7850 (m-30) REVERT: E 249 GLN cc_start: 0.7972 (tt0) cc_final: 0.7178 (mt0) REVERT: F 150 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7862 (tt) REVERT: F 152 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8041 (mt) REVERT: G 138 GLN cc_start: 0.7574 (mp10) cc_final: 0.7165 (mt0) REVERT: G 143 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.4900 (m-80) REVERT: G 228 MET cc_start: 0.8429 (tpp) cc_final: 0.8214 (tpp) REVERT: H 216 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8214 (pp) REVERT: J 249 GLN cc_start: 0.7879 (tt0) cc_final: 0.7476 (mt0) outliers start: 72 outliers final: 62 residues processed: 186 average time/residue: 0.2203 time to fit residues: 59.7798 Evaluate side-chains 204 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain A residue 175 VAL 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 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 141 THR 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 231 THR Chi-restraints excluded: chain E residue 144 LEU 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 E residue 218 SER Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 144 LEU 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 137 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 174 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 21 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 91 optimal weight: 0.1980 overall best weight: 6.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN D 182 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.148795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.123108 restraints weight = 14001.147| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.77 r_work: 0.4147 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4017 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11650 Z= 0.183 Angle : 0.763 12.290 15910 Z= 0.391 Chirality : 0.063 0.470 2010 Planarity : 0.003 0.027 1900 Dihedral : 7.859 55.677 2330 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 6.03 % Allowed : 16.83 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 239 PHE 0.020 0.003 PHE A 171 TYR 0.022 0.002 TYR A 143 ARG 0.002 0.000 ARG I 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 40) link_NAG-ASN : angle 4.16366 ( 120) hydrogen bonds : bond 0.03274 ( 264) hydrogen bonds : angle 5.35633 ( 792) SS BOND : bond 0.00139 ( 10) SS BOND : angle 0.55102 ( 20) covalent geometry : bond 0.00439 (11600) covalent geometry : angle 0.67453 (15770) *********************** REFINEMENT MACRO_CYCLE 9 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 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 133 time to evaluate : 1.318 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: symmetry clash REVERT: A 143 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.4631 (m-80) REVERT: A 152 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 228 MET cc_start: 0.8696 (tpp) cc_final: 0.8320 (tpp) REVERT: A 249 GLN cc_start: 0.8227 (tt0) cc_final: 0.7463 (mt0) REVERT: D 207 MET cc_start: 0.7515 (mtt) cc_final: 0.7202 (mtp) REVERT: E 138 GLN cc_start: 0.7157 (tt0) cc_final: 0.6753 (mp10) REVERT: E 249 GLN cc_start: 0.8153 (tt0) cc_final: 0.7388 (mt0) REVERT: F 150 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7973 (tt) REVERT: F 152 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8138 (mt) REVERT: G 138 GLN cc_start: 0.7686 (mp10) cc_final: 0.7305 (mt0) REVERT: G 143 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: H 216 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8265 (pp) REVERT: J 249 GLN cc_start: 0.8094 (tt0) cc_final: 0.7655 (mt0) outliers start: 76 outliers final: 65 residues processed: 182 average time/residue: 0.2093 time to fit residues: 55.9172 Evaluate side-chains 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 TYR 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 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 B residue 230 VAL Chi-restraints excluded: chain C residue 141 THR 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 208 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 144 LEU 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 E residue 218 SER 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 137 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 174 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.147290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.121785 restraints weight = 13964.803| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.75 r_work: 0.4138 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11650 Z= 0.201 Angle : 0.788 12.659 15910 Z= 0.404 Chirality : 0.063 0.479 2010 Planarity : 0.003 0.026 1900 Dihedral : 7.959 53.163 2330 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.87 % Allowed : 17.06 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 239 PHE 0.021 0.003 PHE A 171 TYR 0.024 0.002 TYR A 143 ARG 0.002 0.000 ARG G 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 40) link_NAG-ASN : angle 4.27168 ( 120) hydrogen bonds : bond 0.03461 ( 264) hydrogen bonds : angle 5.37191 ( 792) SS BOND : bond 0.00139 ( 10) SS BOND : angle 0.60825 ( 20) covalent geometry : bond 0.00484 (11600) covalent geometry : angle 0.69833 (15770) ********************** REFINEMENT MACRO_CYCLE 10 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: 74 poor density : 142 time to evaluate : 1.154 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: symmetry clash REVERT: A 138 GLN cc_start: 0.7448 (mp10) cc_final: 0.6979 (mt0) REVERT: A 143 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.4681 (m-80) REVERT: A 152 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 228 MET cc_start: 0.8662 (tpp) cc_final: 0.8170 (tpp) REVERT: A 247 ARG cc_start: 0.8070 (ttm170) cc_final: 0.7741 (ttm170) REVERT: A 249 GLN cc_start: 0.8260 (tt0) cc_final: 0.7499 (mt0) REVERT: D 207 MET cc_start: 0.7496 (mtt) cc_final: 0.7211 (mtp) REVERT: E 138 GLN cc_start: 0.7139 (tt0) cc_final: 0.6735 (mp10) REVERT: E 249 GLN cc_start: 0.8152 (tt0) cc_final: 0.7427 (mt0) REVERT: F 150 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (tt) REVERT: F 152 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8167 (mt) REVERT: F 247 ARG cc_start: 0.8367 (ttt90) cc_final: 0.8161 (ttt90) REVERT: G 138 GLN cc_start: 0.7576 (mp10) cc_final: 0.7264 (mt0) REVERT: G 143 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.4986 (m-80) REVERT: H 216 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (pp) REVERT: I 249 GLN cc_start: 0.8140 (tt0) cc_final: 0.7455 (mt0) REVERT: J 249 GLN cc_start: 0.8119 (tt0) cc_final: 0.7664 (mt0) outliers start: 74 outliers final: 65 residues processed: 189 average time/residue: 0.2099 time to fit residues: 57.7893 Evaluate side-chains 210 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 139 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 TYR 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 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 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 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 208 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 144 LEU 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 E residue 218 SER 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 137 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 216 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.120827 restraints weight = 14052.612| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.75 r_work: 0.4118 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11650 Z= 0.223 Angle : 0.815 13.108 15910 Z= 0.417 Chirality : 0.064 0.478 2010 Planarity : 0.003 0.025 1900 Dihedral : 8.111 52.646 2330 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.87 % Allowed : 17.38 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 239 PHE 0.022 0.003 PHE A 171 TYR 0.027 0.002 TYR H 143 ARG 0.003 0.000 ARG H 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 40) link_NAG-ASN : angle 4.41442 ( 120) hydrogen bonds : bond 0.03625 ( 264) hydrogen bonds : angle 5.39776 ( 792) SS BOND : bond 0.00121 ( 10) SS BOND : angle 0.61925 ( 20) covalent geometry : bond 0.00538 (11600) covalent geometry : angle 0.72149 (15770) =============================================================================== Job complete usr+sys time: 5287.06 seconds wall clock time: 92 minutes 24.85 seconds (5544.85 seconds total)