Starting phenix.real_space_refine on Fri Jul 3 00:30:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sas_24955/07_2026/7sas_24955.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 4 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.22, per 1000 atoms: 0.11 Number of scatterers: 11420 At special positions: 0 Unit cell: (155.1, 190.3, 49.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2320 8.00 N 1770 7.00 C 7260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS G 214 " - pdb=" SG CYS G 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 214 " - pdb=" SG CYS H 253 " distance=2.03 Simple disulfide: pdb=" SG CYS I 214 " - pdb=" SG CYS I 253 " distance=2.03 Simple disulfide: pdb=" SG CYS J 214 " - pdb=" SG CYS J 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 151 " " NAG A 302 " - " ASN A 164 " " NAG A 303 " - " ASN A 183 " " NAG A 304 " - " ASN A 145 " " NAG B 301 " - " ASN B 151 " " NAG B 302 " - " ASN B 164 " " NAG B 303 " - " ASN B 183 " " NAG B 304 " - " ASN B 145 " " NAG C 301 " - " ASN C 151 " " NAG C 302 " - " ASN C 164 " " NAG C 303 " - " ASN C 183 " " NAG C 304 " - " ASN C 145 " " NAG D 301 " - " ASN D 151 " " NAG D 302 " - " ASN D 164 " " NAG D 303 " - " ASN D 183 " " NAG D 304 " - " ASN D 145 " " NAG E 301 " - " ASN E 151 " " NAG E 302 " - " ASN E 164 " " NAG E 303 " - " ASN E 183 " " NAG E 304 " - " ASN E 145 " " NAG F 301 " - " ASN F 151 " " NAG F 302 " - " ASN F 164 " " NAG F 303 " - " ASN F 183 " " NAG F 304 " - " ASN F 145 " " NAG G 301 " - " ASN G 151 " " NAG G 302 " - " ASN G 164 " " NAG G 303 " - " ASN G 183 " " NAG G 304 " - " ASN G 145 " " NAG H 301 " - " ASN H 151 " " NAG H 302 " - " ASN H 164 " " NAG H 303 " - " ASN H 183 " " NAG H 304 " - " ASN H 145 " " NAG I 301 " - " ASN I 151 " " NAG I 302 " - " ASN I 164 " " NAG I 303 " - " ASN I 183 " " NAG I 304 " - " ASN I 145 " " NAG J 301 " - " ASN J 151 " " NAG J 302 " - " ASN J 164 " " NAG J 303 " - " ASN J 183 " " NAG J 304 " - " ASN J 145 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 252.0 milliseconds 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, 71.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 122 through 126 removed outlier: 6.647A pdb=" N ASP A 122 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR E 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A 124 " --> pdb=" O TYR E 125 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP E 122 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR I 125 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 124 " --> pdb=" O TYR I 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 129 through 138 removed outlier: 8.961A pdb=" N SER D 130 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL H 133 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR D 132 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR H 135 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER D 134 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL H 137 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP D 136 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N SER A 130 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL D 133 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR A 132 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR D 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER A 134 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL D 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP A 136 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER E 130 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA A 131 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR E 132 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER I 130 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA E 131 " --> pdb=" O SER I 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR I 132 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 142 through 143 removed outlier: 6.474A pdb=" N ILE D 142 " --> pdb=" O TYR H 143 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 146 through 160 removed outlier: 6.492A pdb=" N THR D 147 " --> pdb=" O ASN H 148 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU H 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 149 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE H 152 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN D 151 " --> pdb=" O ILE H 152 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN H 154 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR D 153 " --> pdb=" O ASN H 154 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN H 156 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN D 155 " --> pdb=" O ASN H 156 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR H 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR D 157 " --> pdb=" O TYR H 158 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL H 160 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER D 159 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 146 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR E 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 148 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ASN E 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 150 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR E 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 152 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN E 155 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 154 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR E 157 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A 156 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER E 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR A 158 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 163 through 177 removed outlier: 5.706A pdb=" N ASN D 164 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR D 166 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL H 169 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN D 168 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N PHE H 171 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN D 170 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS H 173 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N SER D 172 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL H 175 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR D 174 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N GLY H 177 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE D 176 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN A 164 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA D 167 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 166 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL D 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN A 168 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N PHE D 171 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLN A 170 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LYS D 173 " --> pdb=" O GLN A 170 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N SER A 172 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL D 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR A 174 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY D 177 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE A 176 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA A 167 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN E 168 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 169 " --> pdb=" O GLN E 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN E 170 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE A 171 " --> pdb=" O GLN E 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER E 172 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS A 173 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR E 174 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 175 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 176 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A 177 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA E 167 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN I 168 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL E 169 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 170 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE E 171 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER I 172 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS E 173 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR I 174 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL E 175 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE I 176 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY E 177 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 180 through 187 removed outlier: 7.017A pdb=" N LEU D 181 " --> pdb=" O ARG H 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN H 182 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN D 183 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 181 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN D 182 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A 183 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG A 180 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN E 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN A 182 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR E 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 184 " --> pdb=" O THR E 185 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE E 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 186 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG E 180 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN I 183 " --> pdb=" O ARG E 180 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN E 182 " --> pdb=" O ASN I 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR I 185 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE E 184 " --> pdb=" O THR I 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE I 187 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 186 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 194 through 198 removed outlier: 6.720A pdb=" N ILE A 195 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR E 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 197 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE E 195 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR I 198 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR E 197 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL D 202 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 202 " --> pdb=" O ILE D 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 209 through 230 removed outlier: 7.031A pdb=" N THR D 215 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU H 216 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 217 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER H 218 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE D 219 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE H 224 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL D 225 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU H 226 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET D 227 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET H 228 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 215 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU D 216 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 217 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER D 218 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 219 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE D 224 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 225 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU D 226 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET A 227 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET D 228 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET A 210 " --> pdb=" O TYR E 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE E 213 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 212 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR E 215 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N CYS A 214 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N ILE E 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LEU A 216 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ILE E 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER A 218 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL E 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS A 220 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN E 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N HIS A 222 " --> pdb=" O ASN E 223 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE A 224 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET E 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU A 226 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N GLN E 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET A 228 " --> pdb=" O GLN E 229 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET E 210 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE I 213 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP E 212 " --> pdb=" O PHE I 213 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR I 215 " --> pdb=" O ASP E 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS E 214 " --> pdb=" O THR I 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE I 217 " --> pdb=" O CYS E 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU E 216 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE I 219 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER E 218 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N VAL I 221 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS E 220 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN I 223 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N HIS E 222 " --> pdb=" O ASN I 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL I 225 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE E 224 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET I 227 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU E 226 " --> pdb=" O MET I 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN I 229 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET E 228 " --> pdb=" O GLN I 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 233 through 253 removed outlier: 7.032A pdb=" N VAL H 251 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP D 252 " --> pdb=" O VAL H 251 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 253 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS D 253 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 233 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR E 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 235 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY E 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 237 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER E 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 239 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN E 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU A 241 " --> pdb=" O GLN E 242 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER E 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU E 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN A 245 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR E 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG A 247 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N TYR E 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N GLN A 249 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP E 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL A 251 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 233 " --> pdb=" O THR I 234 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TYR I 236 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 235 " --> pdb=" O TYR I 236 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY I 238 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 237 " --> pdb=" O GLY I 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER I 240 " --> pdb=" O PHE E 237 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS E 239 " --> pdb=" O SER I 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN I 242 " --> pdb=" O HIS E 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU E 241 " --> pdb=" O GLN I 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER I 244 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 243 " --> pdb=" O SER I 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU I 246 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN E 245 " --> pdb=" O GLU I 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR I 248 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG E 247 " --> pdb=" O TYR I 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR I 250 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN E 249 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP I 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL E 251 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 122 through 126 removed outlier: 6.648A pdb=" N ASP C 122 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR G 125 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 124 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP B 122 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR C 125 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS B 124 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 138 removed outlier: 7.007A pdb=" N SER G 130 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA C 131 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR G 132 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER C 130 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA B 131 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR C 132 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N SER B 130 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N VAL F 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR B 132 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR F 135 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 134 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 136 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N SER F 130 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N VAL J 133 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR F 132 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR J 135 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER F 134 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL J 137 " --> pdb=" O SER F 134 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP F 136 " --> pdb=" O VAL J 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 142 through 143 removed outlier: 6.474A pdb=" N ILE B 142 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 142 " --> pdb=" O TYR J 143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 146 through 160 removed outlier: 6.817A pdb=" N ILE C 146 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR G 149 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 148 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN G 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 150 " --> pdb=" O ASN G 151 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR G 153 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 152 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN G 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN C 154 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR G 157 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN C 156 " --> pdb=" O TYR G 157 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N SER G 159 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR C 158 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 163 through 177 removed outlier: 7.068A pdb=" N ALA C 167 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN G 168 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 169 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN G 170 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE C 171 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER G 172 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 173 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR G 174 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 175 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE G 176 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY C 177 " --> pdb=" O ILE G 176 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 167 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN C 168 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 169 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN C 170 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE B 171 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER C 172 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS B 173 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR C 174 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 175 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 176 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B 177 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN B 164 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA F 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR B 166 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N VAL F 169 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN B 168 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N PHE F 171 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN B 170 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS F 173 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N SER B 172 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL F 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR B 174 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY F 177 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE B 176 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN F 164 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA J 167 " --> pdb=" O ASN F 164 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR F 166 " --> pdb=" O ALA J 167 " (cutoff:3.500A) removed outlier: 10.513A pdb=" N VAL J 169 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLN F 168 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N PHE J 171 " --> pdb=" O GLN F 168 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLN F 170 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N LYS J 173 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N SER F 172 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 10.463A pdb=" N VAL J 175 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N THR F 174 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLY J 177 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE F 176 " --> pdb=" O GLY J 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 180 through 187 removed outlier: 9.107A pdb=" N ARG C 180 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N ASN G 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN C 182 " --> pdb=" O ASN G 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR G 185 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE C 184 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE G 187 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 186 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N ASN C 183 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN B 182 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR C 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 184 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 187 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 181 " --> pdb=" O ARG F 180 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN F 182 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN B 183 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU F 181 " --> pdb=" O ARG J 180 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN J 182 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 183 " --> pdb=" O ASN J 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 194 through 198 removed outlier: 6.721A pdb=" N ILE C 195 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR G 198 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 197 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR C 198 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR B 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.403A pdb=" N VAL B 202 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL F 202 " --> pdb=" O ILE J 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 209 through 230 removed outlier: 6.881A pdb=" N MET C 210 " --> pdb=" O TYR G 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE G 213 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 212 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR G 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS C 214 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE G 217 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU C 216 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE G 219 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 218 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL G 221 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 220 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN G 223 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N HIS C 222 " --> pdb=" O ASN G 223 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL G 225 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ILE C 224 " --> pdb=" O VAL G 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET G 227 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU C 226 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN G 229 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET C 228 " --> pdb=" O GLN G 229 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET B 210 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N PHE C 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 212 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N THR C 215 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 214 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE C 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N VAL C 221 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS B 220 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN C 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N HIS B 222 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 225 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE B 224 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N MET C 227 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N LEU B 226 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N GLN C 229 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N MET B 228 " --> pdb=" O GLN C 229 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR B 215 " --> pdb=" O CYS F 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 216 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B 217 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER F 218 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 219 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE F 224 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 225 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU F 226 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET B 227 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET F 228 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR F 215 " --> pdb=" O CYS J 214 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU J 216 " --> pdb=" O THR F 215 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 217 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER J 218 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE F 219 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE J 224 " --> pdb=" O ASN F 223 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL F 225 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU J 226 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET F 227 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET J 228 " --> pdb=" O MET F 227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 233 through 253 removed outlier: 6.716A pdb=" N THR C 233 " --> pdb=" O THR G 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR G 236 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 235 " --> pdb=" O TYR G 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY G 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE C 237 " --> pdb=" O GLY G 238 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER G 240 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS C 239 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN G 242 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU C 241 " --> pdb=" O GLN G 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER G 244 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 243 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLU G 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 245 " --> pdb=" O GLU G 246 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR G 248 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG C 247 " --> pdb=" O TYR G 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR G 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN C 249 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP G 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL C 251 " --> pdb=" O ASP G 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR B 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TYR C 236 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR B 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY C 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N SER C 240 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS B 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLN C 242 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER C 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU C 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR C 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR C 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP B 252 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS F 253 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL J 251 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASP F 252 " --> pdb=" O VAL J 251 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS J 253 " --> pdb=" O ASP F 252 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.90 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: 2675 1.46 - 1.58: 5305 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 11600 Sorted by residual: bond pdb=" N VAL D 123 " pdb=" CA VAL D 123 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.29e-02 6.01e+03 9.22e+00 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 9.17e+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 9.05e+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 9.04e+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 8.98e+00 ... (remaining 11595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15130 1.98 - 3.95: 564 3.95 - 5.93: 56 5.93 - 7.90: 10 7.90 - 9.88: 10 Bond angle restraints: 15770 Sorted by residual: angle pdb=" N LYS B 124 " pdb=" CA LYS B 124 " pdb=" C LYS B 124 " ideal model delta sigma weight residual 108.69 118.57 -9.88 1.77e+00 3.19e-01 3.12e+01 angle pdb=" N LYS G 124 " pdb=" CA LYS G 124 " pdb=" C LYS G 124 " ideal model delta sigma weight residual 108.69 118.57 -9.88 1.77e+00 3.19e-01 3.11e+01 angle pdb=" N LYS D 124 " pdb=" CA LYS D 124 " pdb=" C LYS D 124 " ideal model delta sigma weight residual 108.69 118.56 -9.87 1.77e+00 3.19e-01 3.11e+01 angle pdb=" N LYS C 124 " pdb=" CA LYS C 124 " pdb=" C LYS C 124 " ideal model delta sigma weight residual 108.69 118.54 -9.85 1.77e+00 3.19e-01 3.10e+01 angle pdb=" N LYS J 124 " pdb=" CA LYS J 124 " pdb=" C LYS J 124 " ideal model delta sigma weight residual 108.69 118.53 -9.84 1.77e+00 3.19e-01 3.09e+01 ... (remaining 15765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 5940 14.82 - 29.64: 560 29.64 - 44.46: 120 44.46 - 59.28: 20 59.28 - 74.10: 10 Dihedral angle restraints: 6650 sinusoidal: 2590 harmonic: 4060 Sorted by residual: dihedral pdb=" CA LYS D 139 " pdb=" C LYS D 139 " pdb=" N ARG D 140 " pdb=" CA ARG D 140 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS E 139 " pdb=" C LYS E 139 " pdb=" N ARG E 140 " pdb=" CA ARG E 140 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LYS I 139 " pdb=" C LYS I 139 " pdb=" N ARG I 140 " pdb=" CA ARG I 140 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1514 0.071 - 0.142: 436 0.142 - 0.213: 40 0.213 - 0.284: 0 0.284 - 0.355: 20 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG F 304 " pdb=" ND2 ASN F 145 " pdb=" C2 NAG F 304 " pdb=" O5 NAG F 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG G 304 " pdb=" ND2 ASN G 145 " pdb=" C2 NAG G 304 " pdb=" O5 NAG G 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG E 304 " pdb=" ND2 ASN E 145 " pdb=" C2 NAG E 304 " pdb=" O5 NAG E 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2007 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 138 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C GLN E 138 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN E 138 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS E 139 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 138 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN C 138 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN C 138 " -0.026 2.00e-02 2.50e+03 pdb=" N LYS C 139 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 138 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLN I 138 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN I 138 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS I 139 " 0.023 2.00e-02 2.50e+03 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 209 2.71 - 3.26: 10828 3.26 - 3.81: 17579 3.81 - 4.35: 22389 4.35 - 4.90: 35509 Nonbonded interactions: 86514 Sorted by model distance: nonbonded pdb=" OG1 THR F 231 " pdb=" OG1 THR F 234 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR I 231 " pdb=" OG1 THR I 234 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR B 231 " pdb=" OG1 THR B 234 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 231 " pdb=" OG1 THR A 234 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR J 231 " pdb=" OG1 THR J 234 " model vdw 2.167 3.040 ... (remaining 86509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.120 Check model and map are aligned: 0.050 Set scattering table: 0.010 Process input model: 7.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 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= 0.287 Angle : 1.059 15.444 15910 Z= 0.536 Chirality : 0.070 0.355 2010 Planarity : 0.006 0.039 1900 Dihedral : 12.813 74.103 4020 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.19), 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 ARG 0.001 0.000 ARG G 140 TYR 0.028 0.003 TYR B 157 PHE 0.011 0.003 PHE F 171 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.29 (11600) covalent geometry : angle 0.87033 / 0.50 (15770) SS BOND : bond 0.00265 / 0.19 ( 10) SS BOND : angle 0.51169 / 0.35 ( 20) hydrogen bonds : bond 0.18396 / 12.01 ( 278) hydrogen bonds : angle 11.15566 / 7.55 ( 834) link_NAG-ASN : bond 0.00688 / 0.45 ( 40) link_NAG-ASN : angle 7.00611 / 4.68 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.431 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0641 time to fit residues: 14.0295 Evaluate side-chains 110 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN B 138 GLN B 242 GLN C 138 GLN D 138 GLN D 242 GLN E 138 GLN E 242 GLN F 138 GLN G 138 GLN G 239 HIS H 138 GLN I 138 GLN J 138 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5642 r_free = 0.5642 target = 0.431693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5734 r_free = 0.5734 target = 0.379231 restraints weight = 12524.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5774 r_free = 0.5774 target = 0.376781 restraints weight = 17727.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.5806 r_free = 0.5806 target = 0.372989 restraints weight = 17183.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.5819 r_free = 0.5819 target = 0.372367 restraints weight = 18079.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.5825 r_free = 0.5825 target = 0.371822 restraints weight = 14723.470| |-----------------------------------------------------------------------------| r_work (final): 0.5590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11650 Z= 0.148 Angle : 0.889 13.643 15910 Z= 0.426 Chirality : 0.061 0.373 2010 Planarity : 0.003 0.017 1900 Dihedral : 6.015 17.626 1490 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.25 % Allowed : 10.95 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 247 TYR 0.019 0.002 TYR B 248 PHE 0.016 0.003 PHE D 213 HIS 0.003 0.001 HIS G 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11600) covalent geometry : angle 0.72636 / 0.39 (15770) SS BOND : bond 0.00294 / 0.20 ( 10) SS BOND : angle 0.52992 / 0.37 ( 20) hydrogen bonds : bond 0.04130 / 2.62 ( 278) hydrogen bonds : angle 6.64651 / 4.53 ( 834) link_NAG-ASN : bond 0.00700 / 0.45 ( 40) link_NAG-ASN : angle 5.94217 / 3.97 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.316 Fit side-chains REVERT: E 227 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6324 (tmm) REVERT: H 216 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7960 (pp) outliers start: 41 outliers final: 21 residues processed: 145 average time/residue: 0.0678 time to fit residues: 15.8583 Evaluate side-chains 130 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN E 242 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5564 r_free = 0.5564 target = 0.421416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5688 r_free = 0.5688 target = 0.358235 restraints weight = 12752.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 138)---------------| | r_work = 0.5751 r_free = 0.5751 target = 0.354183 restraints weight = 16362.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 86)----------------| | r_work = 0.5770 r_free = 0.5770 target = 0.351529 restraints weight = 17292.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.5784 r_free = 0.5784 target = 0.351027 restraints weight = 15387.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.5791 r_free = 0.5791 target = 0.350278 restraints weight = 14059.350| |-----------------------------------------------------------------------------| r_work (final): 0.5514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11650 Z= 0.214 Angle : 0.987 16.088 15910 Z= 0.475 Chirality : 0.063 0.372 2010 Planarity : 0.004 0.026 1900 Dihedral : 6.431 18.341 1490 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 5.56 % Allowed : 14.76 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.030 0.003 TYR H 248 PHE 0.019 0.004 PHE B 213 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (11600) covalent geometry : angle 0.82541 / 0.44 (15770) SS BOND : bond 0.00372 / 0.26 ( 10) SS BOND : angle 0.64578 / 0.44 ( 20) hydrogen bonds : bond 0.04115 / 2.63 ( 278) hydrogen bonds : angle 5.86304 / 3.99 ( 834) link_NAG-ASN : bond 0.00758 / 0.48 ( 40) link_NAG-ASN : angle 6.28791 / 4.20 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 125 time to evaluate : 0.437 Fit side-chains REVERT: A 135 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: B 135 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: C 135 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.5640 (m-80) REVERT: D 227 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6679 (mtp) REVERT: F 135 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: F 152 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (mp) REVERT: H 135 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.5103 (m-80) REVERT: H 157 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5990 (m-10) REVERT: H 216 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8037 (pp) REVERT: I 135 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: J 135 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6196 (m-80) outliers start: 70 outliers final: 46 residues processed: 169 average time/residue: 0.0805 time to fit residues: 21.7728 Evaluate side-chains 175 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 157 TYR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 50.0000 chunk 109 optimal weight: 50.0000 chunk 42 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5516 r_free = 0.5516 target = 0.417538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5646 r_free = 0.5646 target = 0.351459 restraints weight = 12923.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.348970 restraints weight = 19156.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.5732 r_free = 0.5732 target = 0.345627 restraints weight = 13928.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 137)---------------| | r_work = 0.5757 r_free = 0.5757 target = 0.343157 restraints weight = 15698.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 105)---------------| | r_work = 0.5768 r_free = 0.5768 target = 0.342298 restraints weight = 17578.420| |-----------------------------------------------------------------------------| r_work (final): 0.5468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11650 Z= 0.242 Angle : 1.015 16.758 15910 Z= 0.497 Chirality : 0.067 0.432 2010 Planarity : 0.004 0.021 1900 Dihedral : 6.622 19.586 1490 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 8.25 % Allowed : 14.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.19), 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 ARG 0.001 0.000 ARG E 140 TYR 0.038 0.004 TYR H 248 PHE 0.019 0.004 PHE B 213 HIS 0.008 0.003 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (11600) covalent geometry : angle 0.86757 / 0.47 (15770) SS BOND : bond 0.00322 / 0.23 ( 10) SS BOND : angle 0.69130 / 0.48 ( 20) hydrogen bonds : bond 0.04231 / 2.75 ( 278) hydrogen bonds : angle 5.61929 / 3.83 ( 834) link_NAG-ASN : bond 0.00995 / 0.63 ( 40) link_NAG-ASN : angle 6.12599 / 4.08 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 128 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: A 145 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7323 (t0) REVERT: B 145 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7456 (t0) REVERT: C 135 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.5570 (m-80) REVERT: C 145 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (t0) REVERT: E 145 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7580 (t0) REVERT: E 178 LYS cc_start: 0.7004 (mttt) cc_final: 0.6023 (tptp) REVERT: F 135 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: F 145 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7732 (t0) REVERT: F 178 LYS cc_start: 0.7654 (mttt) cc_final: 0.6445 (tptp) REVERT: G 145 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7156 (t0) REVERT: H 135 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: H 145 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7228 (t0) REVERT: H 157 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: H 216 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8056 (pp) REVERT: I 135 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: I 145 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6995 (t0) REVERT: I 175 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7198 (t) REVERT: J 135 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6266 (m-80) REVERT: J 145 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7187 (t0) outliers start: 104 outliers final: 60 residues processed: 203 average time/residue: 0.0778 time to fit residues: 25.3032 Evaluate side-chains 197 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 119 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 157 TYR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5532 r_free = 0.5532 target = 0.419707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5682 r_free = 0.5682 target = 0.352800 restraints weight = 12894.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5716 r_free = 0.5716 target = 0.350971 restraints weight = 20281.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.5740 r_free = 0.5740 target = 0.348590 restraints weight = 17294.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5759 r_free = 0.5759 target = 0.347162 restraints weight = 16866.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.5771 r_free = 0.5771 target = 0.346091 restraints weight = 17726.903| |-----------------------------------------------------------------------------| r_work (final): 0.5482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11650 Z= 0.196 Angle : 0.906 16.503 15910 Z= 0.448 Chirality : 0.064 0.389 2010 Planarity : 0.004 0.026 1900 Dihedral : 6.400 19.642 1490 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 6.27 % Allowed : 16.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 140 TYR 0.029 0.003 TYR H 248 PHE 0.015 0.003 PHE B 213 HIS 0.007 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (11600) covalent geometry : angle 0.77944 / 0.42 (15770) SS BOND : bond 0.00269 / 0.19 ( 10) SS BOND : angle 0.52945 / 0.36 ( 20) hydrogen bonds : bond 0.03738 / 2.41 ( 278) hydrogen bonds : angle 5.57447 / 3.80 ( 834) link_NAG-ASN : bond 0.00841 / 0.53 ( 40) link_NAG-ASN : angle 5.38079 / 3.56 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 130 time to evaluate : 0.421 Fit side-chains REVERT: A 135 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.4989 (m-80) REVERT: A 145 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 135 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: B 145 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7303 (t0) REVERT: C 135 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.5593 (m-80) REVERT: C 145 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (t0) REVERT: C 150 LEU cc_start: 0.8610 (mp) cc_final: 0.8313 (mp) REVERT: C 178 LYS cc_start: 0.7551 (mttt) cc_final: 0.6138 (tptp) REVERT: C 211 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5669 (m-10) REVERT: D 145 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7438 (t0) REVERT: D 178 LYS cc_start: 0.7295 (mttt) cc_final: 0.7073 (mttp) REVERT: E 145 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7144 (t0) REVERT: E 178 LYS cc_start: 0.6934 (mttt) cc_final: 0.5944 (tptp) REVERT: F 145 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7325 (t0) REVERT: F 178 LYS cc_start: 0.7519 (mttt) cc_final: 0.6347 (tptp) REVERT: F 211 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6007 (m-10) REVERT: G 145 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7022 (t0) REVERT: H 135 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: H 145 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7116 (t0) REVERT: H 150 LEU cc_start: 0.8549 (mp) cc_final: 0.8262 (mp) REVERT: H 211 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: H 216 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8114 (pp) REVERT: I 145 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.6879 (t0) REVERT: J 135 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6053 (m-80) outliers start: 79 outliers final: 55 residues processed: 183 average time/residue: 0.0807 time to fit residues: 23.4196 Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 126 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 59 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 170 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN J 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5521 r_free = 0.5521 target = 0.419306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5697 r_free = 0.5697 target = 0.349362 restraints weight = 12937.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5705 r_free = 0.5705 target = 0.347648 restraints weight = 21620.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5716 r_free = 0.5716 target = 0.347769 restraints weight = 20190.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5727 r_free = 0.5727 target = 0.347176 restraints weight = 16230.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5736 r_free = 0.5736 target = 0.346568 restraints weight = 18273.785| |-----------------------------------------------------------------------------| r_work (final): 0.5475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11650 Z= 0.208 Angle : 0.911 16.526 15910 Z= 0.455 Chirality : 0.065 0.432 2010 Planarity : 0.004 0.022 1900 Dihedral : 6.408 19.403 1490 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 7.86 % Allowed : 15.63 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 247 TYR 0.031 0.003 TYR H 248 PHE 0.016 0.003 PHE I 213 HIS 0.007 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (11600) covalent geometry : angle 0.78805 / 0.43 (15770) SS BOND : bond 0.00251 / 0.18 ( 10) SS BOND : angle 0.55099 / 0.38 ( 20) hydrogen bonds : bond 0.03858 / 2.50 ( 278) hydrogen bonds : angle 5.56865 / 3.80 ( 834) link_NAG-ASN : bond 0.00866 / 0.53 ( 40) link_NAG-ASN : angle 5.31742 / 3.51 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 0.417 Fit side-chains REVERT: A 135 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.4807 (m-80) REVERT: A 145 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7253 (t0) REVERT: A 150 LEU cc_start: 0.8588 (mp) cc_final: 0.8309 (mp) REVERT: B 135 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: B 145 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7384 (t0) REVERT: C 135 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: C 145 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7464 (t0) REVERT: C 150 LEU cc_start: 0.8620 (mp) cc_final: 0.8330 (mp) REVERT: C 178 LYS cc_start: 0.7615 (mttt) cc_final: 0.6195 (tptp) REVERT: C 211 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.5735 (m-10) REVERT: D 145 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (t0) REVERT: E 126 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7621 (mt) REVERT: E 145 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7278 (t0) REVERT: E 178 LYS cc_start: 0.7002 (mttt) cc_final: 0.6020 (tptp) REVERT: F 135 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: F 145 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7505 (t0) REVERT: F 178 LYS cc_start: 0.7581 (mttt) cc_final: 0.6369 (tptp) REVERT: F 211 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6151 (m-10) REVERT: G 145 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7110 (t0) REVERT: H 135 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.5642 (m-80) REVERT: H 145 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7215 (t0) REVERT: H 150 LEU cc_start: 0.8621 (mp) cc_final: 0.8349 (mp) REVERT: H 178 LYS cc_start: 0.7749 (mttt) cc_final: 0.6567 (tptp) REVERT: H 211 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6492 (m-10) REVERT: H 216 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8097 (pp) REVERT: I 135 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6327 (m-80) REVERT: I 145 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7009 (t0) REVERT: J 135 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: J 145 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7119 (t0) REVERT: J 178 LYS cc_start: 0.7495 (mttt) cc_final: 0.6180 (tptp) outliers start: 99 outliers final: 71 residues processed: 203 average time/residue: 0.0846 time to fit residues: 26.8199 Evaluate side-chains 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 133 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 54 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 overall best weight: 17.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN C 249 GLN D 242 GLN E 170 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN G 242 GLN G 249 GLN I 170 GLN J 138 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5458 r_free = 0.5458 target = 0.408650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5565 r_free = 0.5565 target = 0.340099 restraints weight = 13148.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5601 r_free = 0.5601 target = 0.337715 restraints weight = 22108.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5626 r_free = 0.5626 target = 0.335245 restraints weight = 17666.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.5653 r_free = 0.5653 target = 0.332646 restraints weight = 17801.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5656 r_free = 0.5656 target = 0.332305 restraints weight = 18942.803| |-----------------------------------------------------------------------------| r_work (final): 0.5406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 11650 Z= 0.378 Angle : 1.137 17.530 15910 Z= 0.582 Chirality : 0.073 0.457 2010 Planarity : 0.005 0.028 1900 Dihedral : 7.271 21.069 1490 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 10.32 % Allowed : 14.05 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.18), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 247 TYR 0.050 0.006 TYR C 248 PHE 0.026 0.006 PHE J 213 HIS 0.012 0.003 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.38 (11600) covalent geometry : angle 1.01468 / 0.56 (15770) SS BOND : bond 0.00267 / 0.19 ( 10) SS BOND : angle 0.97165 / 0.67 ( 20) hydrogen bonds : bond 0.05628 / 3.71 ( 278) hydrogen bonds : angle 5.89149 / 4.02 ( 834) link_NAG-ASN : bond 0.01073 / 0.67 ( 40) link_NAG-ASN : angle 6.00559 / 3.97 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 142 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: A 150 LEU cc_start: 0.8537 (mp) cc_final: 0.8199 (mp) REVERT: B 145 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 178 LYS cc_start: 0.7416 (mttt) cc_final: 0.6227 (tptp) REVERT: B 216 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8521 (pp) REVERT: C 135 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.5330 (m-80) REVERT: C 145 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7462 (t0) REVERT: C 150 LEU cc_start: 0.8593 (mp) cc_final: 0.8279 (mp) REVERT: C 178 LYS cc_start: 0.7543 (mttt) cc_final: 0.6390 (tptp) REVERT: C 211 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6174 (m-10) REVERT: D 145 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7430 (t0) REVERT: D 178 LYS cc_start: 0.7139 (mttt) cc_final: 0.6509 (tptp) REVERT: E 126 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7859 (mt) REVERT: E 178 LYS cc_start: 0.6834 (mttt) cc_final: 0.6283 (tptp) REVERT: F 135 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6785 (m-80) REVERT: F 145 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7513 (t0) REVERT: F 178 LYS cc_start: 0.7604 (mttt) cc_final: 0.6627 (tptp) REVERT: F 211 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6335 (m-10) REVERT: G 145 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7095 (t0) REVERT: G 178 LYS cc_start: 0.7585 (mttt) cc_final: 0.6180 (tptp) REVERT: H 135 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: H 150 LEU cc_start: 0.8504 (mp) cc_final: 0.8252 (mp) REVERT: H 157 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6954 (m-10) REVERT: H 178 LYS cc_start: 0.7672 (mttt) cc_final: 0.6678 (tptp) REVERT: H 211 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: I 135 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: I 145 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7181 (t0) REVERT: I 178 LYS cc_start: 0.7637 (mttt) cc_final: 0.7354 (mttp) REVERT: J 178 LYS cc_start: 0.7571 (mttt) cc_final: 0.6394 (tptp) REVERT: J 246 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6832 (pm20) outliers start: 130 outliers final: 92 residues processed: 241 average time/residue: 0.0846 time to fit residues: 31.5578 Evaluate side-chains 242 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 132 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL 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 227 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 211 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain G residue 135 TYR Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 211 TYR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 157 TYR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 211 TYR Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 211 TYR Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 244 SER Chi-restraints excluded: chain J residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 121 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN I 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5546 r_free = 0.5546 target = 0.423912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5685 r_free = 0.5685 target = 0.354895 restraints weight = 12920.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5720 r_free = 0.5720 target = 0.351709 restraints weight = 21293.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 85)----------------| | r_work = 0.5753 r_free = 0.5753 target = 0.348949 restraints weight = 17373.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.5762 r_free = 0.5762 target = 0.347690 restraints weight = 18015.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 93)----------------| | r_work = 0.5779 r_free = 0.5779 target = 0.346965 restraints weight = 15688.644| |-----------------------------------------------------------------------------| r_work (final): 0.5497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4594 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= 0.163 Angle : 0.861 16.223 15910 Z= 0.428 Chirality : 0.065 0.465 2010 Planarity : 0.003 0.027 1900 Dihedral : 6.380 19.249 1490 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 6.35 % Allowed : 17.70 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.18), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 140 TYR 0.020 0.002 TYR A 248 PHE 0.014 0.003 PHE B 237 HIS 0.006 0.002 HIS G 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (11600) covalent geometry : angle 0.74435 / 0.40 (15770) SS BOND : bond 0.00144 / 0.10 ( 10) SS BOND : angle 0.47108 / 0.33 ( 20) hydrogen bonds : bond 0.03352 / 2.16 ( 278) hydrogen bonds : angle 5.73543 / 3.93 ( 834) link_NAG-ASN : bond 0.00811 / 0.49 ( 40) link_NAG-ASN : angle 5.03490 / 3.35 ( 120) *********************** 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 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 146 time to evaluate : 0.345 Fit side-chains REVERT: A 145 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.6906 (t0) REVERT: B 145 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.6955 (t0) REVERT: B 216 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8385 (pp) REVERT: C 135 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.5444 (m-80) REVERT: C 150 LEU cc_start: 0.8592 (mp) cc_final: 0.8389 (mp) REVERT: C 178 LYS cc_start: 0.7364 (mttt) cc_final: 0.6206 (tptp) REVERT: D 178 LYS cc_start: 0.7201 (mttt) cc_final: 0.6292 (tptp) REVERT: E 126 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7708 (mt) REVERT: E 145 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7183 (t0) REVERT: E 178 LYS cc_start: 0.6900 (mttt) cc_final: 0.5939 (tptp) REVERT: F 145 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7312 (t0) REVERT: F 161 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7183 (mm-30) REVERT: F 178 LYS cc_start: 0.7474 (mttt) cc_final: 0.6496 (tptp) REVERT: G 145 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7172 (t0) REVERT: G 178 LYS cc_start: 0.7391 (mttt) cc_final: 0.5936 (tptp) REVERT: H 135 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: H 145 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7335 (t0) REVERT: H 150 LEU cc_start: 0.8579 (mp) cc_final: 0.8309 (mp) REVERT: H 178 LYS cc_start: 0.7568 (mttt) cc_final: 0.6493 (tptp) REVERT: H 216 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8017 (pp) REVERT: I 145 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.6846 (t0) REVERT: J 145 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7205 (t0) REVERT: J 178 LYS cc_start: 0.7460 (mttt) cc_final: 0.6205 (tptp) outliers start: 80 outliers final: 61 residues processed: 197 average time/residue: 0.0857 time to fit residues: 26.2456 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 143 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 120 optimal weight: 20.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5502 r_free = 0.5502 target = 0.414747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5631 r_free = 0.5631 target = 0.344171 restraints weight = 12975.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5637 r_free = 0.5637 target = 0.343243 restraints weight = 20920.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5667 r_free = 0.5667 target = 0.341079 restraints weight = 19058.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.5682 r_free = 0.5682 target = 0.339155 restraints weight = 18671.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.5698 r_free = 0.5698 target = 0.338257 restraints weight = 17748.335| |-----------------------------------------------------------------------------| r_work (final): 0.5453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11650 Z= 0.266 Angle : 0.999 16.756 15910 Z= 0.507 Chirality : 0.069 0.479 2010 Planarity : 0.004 0.030 1900 Dihedral : 6.730 19.630 1490 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 7.14 % Allowed : 17.14 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.18), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.034 0.004 TYR A 248 PHE 0.019 0.004 PHE I 213 HIS 0.008 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.26 (11600) covalent geometry : angle 0.88288 / 0.48 (15770) SS BOND : bond 0.00178 / 0.12 ( 10) SS BOND : angle 0.74821 / 0.51 ( 20) hydrogen bonds : bond 0.04527 / 2.97 ( 278) hydrogen bonds : angle 5.70692 / 3.91 ( 834) link_NAG-ASN : bond 0.01204 / 0.75 ( 40) link_NAG-ASN : angle 5.45037 / 3.56 ( 120) *********************** 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 235 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 145 time to evaluate : 0.437 Fit side-chains REVERT: A 135 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.4779 (m-80) REVERT: A 145 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7010 (t0) REVERT: B 135 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: B 145 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.6979 (t0) REVERT: B 178 LYS cc_start: 0.7262 (mttt) cc_final: 0.6104 (tptp) REVERT: B 216 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8380 (pp) REVERT: C 135 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.5440 (m-80) REVERT: C 150 LEU cc_start: 0.8588 (mp) cc_final: 0.8340 (mp) REVERT: C 178 LYS cc_start: 0.7512 (mttt) cc_final: 0.6352 (tptp) REVERT: D 178 LYS cc_start: 0.7046 (mttt) cc_final: 0.6486 (tptp) REVERT: E 126 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7844 (mt) REVERT: E 145 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7280 (t0) REVERT: E 178 LYS cc_start: 0.6907 (mttt) cc_final: 0.6200 (tptp) REVERT: E 211 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.6725 (m-10) REVERT: F 135 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6784 (m-80) REVERT: F 145 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7463 (t0) REVERT: F 178 LYS cc_start: 0.7563 (mttt) cc_final: 0.6644 (tptp) REVERT: G 145 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7060 (t0) REVERT: G 178 LYS cc_start: 0.7492 (mttt) cc_final: 0.6185 (tptp) REVERT: H 135 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: H 145 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7105 (t0) REVERT: H 150 LEU cc_start: 0.8481 (mp) cc_final: 0.8152 (mp) REVERT: H 178 LYS cc_start: 0.7611 (mttt) cc_final: 0.6632 (tptp) REVERT: H 216 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8030 (pp) REVERT: I 145 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6893 (t0) REVERT: I 178 LYS cc_start: 0.7610 (mttt) cc_final: 0.7373 (mttp) REVERT: J 135 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6240 (m-80) REVERT: J 145 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7210 (t0) REVERT: J 178 LYS cc_start: 0.7563 (mttt) cc_final: 0.6427 (tptp) outliers start: 90 outliers final: 69 residues processed: 203 average time/residue: 0.0858 time to fit residues: 26.9758 Evaluate side-chains 226 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 139 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL 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 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 211 TYR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 135 TYR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 231 THR Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 35 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5561 r_free = 0.5561 target = 0.424598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5697 r_free = 0.5697 target = 0.354498 restraints weight = 12937.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5735 r_free = 0.5735 target = 0.352244 restraints weight = 21962.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5752 r_free = 0.5752 target = 0.350413 restraints weight = 18724.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5770 r_free = 0.5770 target = 0.349062 restraints weight = 15957.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.5781 r_free = 0.5781 target = 0.348005 restraints weight = 16700.717| |-----------------------------------------------------------------------------| r_work (final): 0.5514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11650 Z= 0.157 Angle : 0.852 15.980 15910 Z= 0.426 Chirality : 0.065 0.558 2010 Planarity : 0.003 0.025 1900 Dihedral : 6.209 18.864 1490 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 6.11 % Allowed : 17.78 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.18), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 247 TYR 0.027 0.002 TYR B 143 PHE 0.013 0.003 PHE B 237 HIS 0.006 0.002 HIS G 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11600) covalent geometry : angle 0.73981 / 0.40 (15770) SS BOND : bond 0.00136 / 0.09 ( 10) SS BOND : angle 0.44501 / 0.31 ( 20) hydrogen bonds : bond 0.03233 / 2.10 ( 278) hydrogen bonds : angle 5.60555 / 3.84 ( 834) link_NAG-ASN : bond 0.01002 / 0.63 ( 40) link_NAG-ASN : angle 4.91666 / 3.23 ( 120) ********************** 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 227 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 0.442 Fit side-chains REVERT: A 145 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7251 (t0) REVERT: B 145 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.6823 (t0) REVERT: B 178 LYS cc_start: 0.7299 (mttt) cc_final: 0.5901 (tptp) REVERT: B 216 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8347 (pp) REVERT: B 228 MET cc_start: 0.7639 (tpp) cc_final: 0.7374 (mmt) REVERT: C 135 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: C 178 LYS cc_start: 0.7382 (mttt) cc_final: 0.6208 (tptp) REVERT: D 178 LYS cc_start: 0.6973 (mttt) cc_final: 0.6379 (tptp) REVERT: E 126 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7697 (mt) REVERT: E 145 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7261 (t0) REVERT: E 178 LYS cc_start: 0.6895 (mttt) cc_final: 0.5958 (tptp) REVERT: F 161 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7204 (mm-30) REVERT: F 178 LYS cc_start: 0.7389 (mttt) cc_final: 0.6473 (tptp) REVERT: G 145 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7101 (t0) REVERT: G 178 LYS cc_start: 0.7415 (mttt) cc_final: 0.5995 (tptp) REVERT: H 145 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7263 (t0) REVERT: H 178 LYS cc_start: 0.7598 (mttt) cc_final: 0.6529 (tptp) REVERT: H 216 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8017 (pp) REVERT: I 145 ASN cc_start: 0.7549 (OUTLIER) cc_final: 0.6899 (t0) REVERT: J 145 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7113 (t0) REVERT: J 178 LYS cc_start: 0.7386 (mttt) cc_final: 0.6291 (tptp) outliers start: 77 outliers final: 63 residues processed: 197 average time/residue: 0.0873 time to fit residues: 26.7152 Evaluate side-chains 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 143 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 VAL 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 231 THR Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 144 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 145 ASN Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 182 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 145 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 182 ASN Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain J residue 244 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 1 optimal weight: 20.0000 chunk 112 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 overall best weight: 3.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5607 r_free = 0.5607 target = 0.431282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5738 r_free = 0.5738 target = 0.362717 restraints weight = 12824.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5781 r_free = 0.5781 target = 0.360188 restraints weight = 22237.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.5805 r_free = 0.5805 target = 0.357654 restraints weight = 18549.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.5829 r_free = 0.5829 target = 0.355713 restraints weight = 18209.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.5839 r_free = 0.5839 target = 0.354815 restraints weight = 18396.908| |-----------------------------------------------------------------------------| r_work (final): 0.5557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11650 Z= 0.127 Angle : 0.780 14.397 15910 Z= 0.391 Chirality : 0.062 0.462 2010 Planarity : 0.003 0.030 1900 Dihedral : 5.899 19.150 1490 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.40 % Allowed : 18.49 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 247 TYR 0.022 0.002 TYR B 143 PHE 0.018 0.002 PHE B 237 HIS 0.006 0.001 HIS G 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11600) covalent geometry : angle 0.68007 / 0.37 (15770) SS BOND : bond 0.00122 / 0.08 ( 10) SS BOND : angle 0.31624 / 0.24 ( 20) hydrogen bonds : bond 0.02723 / 1.75 ( 278) hydrogen bonds : angle 5.50361 / 3.78 ( 834) link_NAG-ASN : bond 0.00882 / 0.58 ( 40) link_NAG-ASN : angle 4.46155 / 2.94 ( 120) =============================================================================== Job complete usr+sys time: 1856.33 seconds wall clock time: 33 minutes 19.55 seconds (1999.55 seconds total)