Starting phenix.real_space_refine on Sun Dec 29 18:33:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_24955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_24955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_24955.map" model { file = "/net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_24955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sas_24955/12_2024/7sas_24955.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11420 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.27, per 1000 atoms: 0.29 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 71.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 3.32 Time building geometry restraints manager: 3.04 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: 6651 14.82 - 29.64: 602 29.64 - 44.46: 120 44.46 - 59.28: 80 59.28 - 74.10: 10 Dihedral angle restraints: 7463 sinusoidal: 3403 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 7460 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: 2.03 - 2.61: 87 2.61 - 3.18: 9872 3.18 - 3.75: 16213 3.75 - 4.33: 23612 4.33 - 4.90: 36757 Nonbonded interactions: 86541 Sorted by model distance: nonbonded pdb=" SG CYS I 214 " pdb=" SG CYS I 253 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS F 214 " pdb=" SG CYS F 253 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 214 " pdb=" SG CYS D 253 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 214 " pdb=" SG CYS B 253 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS J 214 " pdb=" SG CYS J 253 " model vdw 2.034 3.760 ... (remaining 86536 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: 0.00 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.570 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 11600 Z= 0.324 Angle : 0.870 9.879 15770 Z= 0.499 Chirality : 0.070 0.355 2010 Planarity : 0.006 0.039 1900 Dihedral : 13.331 74.103 4860 Min Nonbonded Distance : 2.033 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.19), 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 HIS 0.003 0.001 HIS B 239 PHE 0.011 0.003 PHE F 171 TYR 0.028 0.003 TYR B 157 ARG 0.001 0.000 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1719 time to fit residues: 36.6613 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 : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 20.0000 chunk 98 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN B 242 GLN D 138 GLN D 242 GLN E 138 GLN E 242 GLN F 138 GLN G 138 GLN H 138 GLN I 138 GLN J 138 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11600 Z= 0.210 Angle : 0.711 7.638 15770 Z= 0.386 Chirality : 0.061 0.378 2010 Planarity : 0.003 0.017 1900 Dihedral : 8.275 47.083 2330 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 3.17 % Allowed : 10.87 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 239 PHE 0.021 0.004 PHE E 213 TYR 0.020 0.002 TYR H 248 ARG 0.001 0.000 ARG F 247 *********************** 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 162 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 1.392 Fit side-chains REVERT: E 227 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6128 (tmm) outliers start: 40 outliers final: 20 residues processed: 148 average time/residue: 0.1699 time to fit residues: 40.2946 Evaluate side-chains 125 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 160 VAL Chi-restraints excluded: chain H residue 231 THR 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 65 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 182 ASN B 239 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN E 242 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS H 138 GLN I 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11600 Z= 0.248 Angle : 0.707 7.684 15770 Z= 0.386 Chirality : 0.059 0.363 2010 Planarity : 0.003 0.024 1900 Dihedral : 8.293 46.450 2330 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 3.81 % Allowed : 15.16 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 239 PHE 0.018 0.003 PHE B 213 TYR 0.023 0.003 TYR D 248 ARG 0.001 0.000 ARG B 140 *********************** 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 173 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 1.137 Fit side-chains REVERT: D 227 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6819 (mtp) outliers start: 48 outliers final: 34 residues processed: 151 average time/residue: 0.1779 time to fit residues: 42.7840 Evaluate side-chains 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 160 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 160 VAL 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 207 MET 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 E residue 160 VAL 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 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 207 MET Chi-restraints excluded: chain H residue 147 THR 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 I residue 138 GLN Chi-restraints excluded: chain I residue 160 VAL 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 116 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 chunk 61 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 56 optimal weight: 50.0000 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 182 ASN D 138 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 ASN H 239 HIS H 249 GLN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN J 249 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11600 Z= 0.193 Angle : 0.661 7.522 15770 Z= 0.359 Chirality : 0.058 0.408 2010 Planarity : 0.003 0.018 1900 Dihedral : 7.938 45.473 2330 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 5.32 % Allowed : 14.84 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.20), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 239 PHE 0.014 0.003 PHE F 213 TYR 0.018 0.002 TYR H 248 ARG 0.003 0.000 ARG B 180 *********************** 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 197 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 130 time to evaluate : 1.218 Fit side-chains REVERT: A 145 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7458 (t0) REVERT: D 227 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6695 (mtp) REVERT: E 214 CYS cc_start: 0.7613 (t) cc_final: 0.7302 (t) REVERT: G 145 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7478 (t0) REVERT: I 145 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7168 (t0) outliers start: 67 outliers final: 45 residues processed: 168 average time/residue: 0.1737 time to fit residues: 46.7861 Evaluate side-chains 174 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 GLN Chi-restraints excluded: chain A residue 145 ASN 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 B residue 138 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 227 MET 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 233 THR Chi-restraints excluded: chain D residue 138 GLN 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 207 MET 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 E residue 160 VAL Chi-restraints excluded: chain E residue 175 VAL 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 175 VAL Chi-restraints excluded: chain F residue 182 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 230 VAL 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 207 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain H residue 160 VAL 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 216 LEU Chi-restraints excluded: chain J residue 138 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN D 249 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11600 Z= 0.377 Angle : 0.839 11.270 15770 Z= 0.459 Chirality : 0.063 0.384 2010 Planarity : 0.004 0.028 1900 Dihedral : 8.826 49.571 2330 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 6.67 % Allowed : 15.48 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.017 0.004 PHE I 213 TYR 0.039 0.004 TYR H 248 ARG 0.001 0.000 ARG B 140 *********************** 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 222 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 138 time to evaluate : 1.258 Fit side-chains REVERT: A 135 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: A 145 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7412 (t0) REVERT: B 145 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7472 (t0) REVERT: B 182 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6937 (p0) REVERT: C 135 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: C 150 LEU cc_start: 0.8422 (mp) cc_final: 0.8157 (mp) REVERT: D 145 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7678 (t0) REVERT: D 214 CYS cc_start: 0.8001 (t) cc_final: 0.7555 (t) REVERT: D 227 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6927 (mtp) REVERT: E 145 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7459 (t0) REVERT: E 178 LYS cc_start: 0.7383 (mttt) cc_final: 0.6353 (tptp) REVERT: E 214 CYS cc_start: 0.7744 (t) cc_final: 0.7442 (t) REVERT: F 135 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: F 145 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7676 (t0) REVERT: F 178 LYS cc_start: 0.7875 (mttt) cc_final: 0.6793 (tptp) REVERT: G 145 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7175 (t0) REVERT: G 242 GLN cc_start: 0.7668 (mt0) cc_final: 0.7462 (mt0) REVERT: H 135 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.5404 (m-80) REVERT: H 145 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7433 (t0) REVERT: I 145 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7088 (t0) REVERT: J 135 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: J 145 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7265 (t0) outliers start: 84 outliers final: 55 residues processed: 198 average time/residue: 0.1848 time to fit residues: 56.7424 Evaluate side-chains 198 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 127 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 144 LEU Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 ASN 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 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 SER 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 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 144 LEU Chi-restraints excluded: chain E residue 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 175 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 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 216 LEU 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 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 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 175 VAL 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 147 THR Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain J residue 135 TYR 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 163 GLU 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 42 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN B 182 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11600 Z= 0.278 Angle : 0.750 12.051 15770 Z= 0.408 Chirality : 0.060 0.450 2010 Planarity : 0.003 0.022 1900 Dihedral : 8.488 52.796 2330 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.90 % Allowed : 16.11 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.015 0.003 PHE I 213 TYR 0.029 0.003 TYR H 248 ARG 0.001 0.000 ARG D 247 *********************** 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 225 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 138 time to evaluate : 1.202 Fit side-chains REVERT: A 135 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: A 145 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7458 (t0) REVERT: B 135 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: B 145 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7447 (t0) REVERT: D 145 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7717 (t0) REVERT: D 214 CYS cc_start: 0.8041 (t) cc_final: 0.7571 (t) REVERT: D 227 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: E 145 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7425 (t0) REVERT: E 178 LYS cc_start: 0.7315 (mttt) cc_final: 0.6314 (tptp) REVERT: E 214 CYS cc_start: 0.7724 (t) cc_final: 0.7437 (t) REVERT: F 135 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: F 145 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7680 (t0) REVERT: F 178 LYS cc_start: 0.7855 (mttt) cc_final: 0.6808 (tptp) REVERT: G 145 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7369 (t0) REVERT: H 135 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: H 145 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7475 (t0) REVERT: H 150 LEU cc_start: 0.8475 (mp) cc_final: 0.8190 (mp) REVERT: H 228 MET cc_start: 0.8066 (tpp) cc_final: 0.7753 (tpp) REVERT: I 135 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: I 145 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7110 (t0) REVERT: J 135 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: J 145 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7208 (t0) outliers start: 87 outliers final: 58 residues processed: 192 average time/residue: 0.1933 time to fit residues: 58.0843 Evaluate side-chains 206 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 132 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 144 LEU 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 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 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 145 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR 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 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 216 LEU 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 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 210 MET Chi-restraints excluded: chain H residue 216 LEU 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 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 163 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.2980 chunk 14 optimal weight: 30.0000 chunk 71 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 125 optimal weight: 30.0000 chunk 78 optimal weight: 0.5980 chunk 76 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN J 170 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11600 Z= 0.208 Angle : 0.695 11.880 15770 Z= 0.374 Chirality : 0.059 0.433 2010 Planarity : 0.003 0.019 1900 Dihedral : 8.311 62.487 2330 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 6.67 % Allowed : 16.19 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 239 PHE 0.014 0.003 PHE B 237 TYR 0.020 0.002 TYR H 248 ARG 0.001 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 136 time to evaluate : 1.254 Fit side-chains REVERT: A 145 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7561 (t0) REVERT: B 145 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7631 (t0) REVERT: D 214 CYS cc_start: 0.8020 (t) cc_final: 0.7604 (t) REVERT: E 178 LYS cc_start: 0.7233 (mttt) cc_final: 0.6286 (tptp) REVERT: E 214 CYS cc_start: 0.7797 (t) cc_final: 0.7534 (t) REVERT: F 178 LYS cc_start: 0.7826 (mttt) cc_final: 0.6787 (tptp) REVERT: G 145 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7389 (t0) REVERT: H 145 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (t0) REVERT: H 228 MET cc_start: 0.8223 (tpp) cc_final: 0.7863 (tpp) REVERT: I 145 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7291 (t0) REVERT: J 145 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7330 (t0) outliers start: 84 outliers final: 59 residues processed: 187 average time/residue: 0.1842 time to fit residues: 53.7746 Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 134 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 174 THR 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 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 144 LEU 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 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 144 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 144 LEU 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 216 LEU Chi-restraints excluded: chain F residue 230 VAL 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 207 MET 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 216 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 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 244 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11600 Z= 0.343 Angle : 0.826 11.686 15770 Z= 0.450 Chirality : 0.063 0.445 2010 Planarity : 0.004 0.032 1900 Dihedral : 8.889 77.676 2330 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 6.03 % Allowed : 16.83 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.016 0.004 PHE I 213 TYR 0.034 0.004 TYR H 248 ARG 0.001 0.000 ARG D 247 *********************** 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 217 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 1.194 Fit side-chains REVERT: A 135 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: A 145 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7308 (t0) REVERT: A 150 LEU cc_start: 0.8334 (mp) cc_final: 0.8115 (mp) REVERT: B 145 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7286 (t0) REVERT: C 178 LYS cc_start: 0.7799 (mttt) cc_final: 0.6714 (tptp) REVERT: D 214 CYS cc_start: 0.8051 (t) cc_final: 0.7650 (t) REVERT: E 178 LYS cc_start: 0.7154 (mttt) cc_final: 0.6482 (tptp) REVERT: E 214 CYS cc_start: 0.7748 (t) cc_final: 0.7405 (t) REVERT: E 216 LEU cc_start: 0.8430 (pp) cc_final: 0.8178 (pp) REVERT: F 178 LYS cc_start: 0.7702 (mttt) cc_final: 0.6807 (tptp) REVERT: G 145 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7519 (t0) REVERT: H 135 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.5435 (m-80) REVERT: H 145 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7403 (t0) REVERT: H 228 MET cc_start: 0.8220 (tpp) cc_final: 0.7858 (tpp) REVERT: I 145 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7036 (t0) REVERT: J 145 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7337 (t0) outliers start: 76 outliers final: 64 residues processed: 187 average time/residue: 0.1854 time to fit residues: 53.4185 Evaluate side-chains 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 174 THR 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 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain C residue 144 LEU 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 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 144 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR 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 144 LEU 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 216 LEU 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 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 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 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 163 GLU 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 109 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** C 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** I 170 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11600 Z= 0.303 Angle : 0.781 9.429 15770 Z= 0.427 Chirality : 0.061 0.440 2010 Planarity : 0.004 0.030 1900 Dihedral : 9.168 96.920 2330 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 6.03 % Allowed : 16.83 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.015 0.003 PHE I 213 TYR 0.029 0.003 TYR H 248 ARG 0.004 0.000 ARG B 180 *********************** 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 221 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 145 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: A 145 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 150 LEU cc_start: 0.8302 (mp) cc_final: 0.8088 (mp) REVERT: B 145 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7368 (t0) REVERT: C 178 LYS cc_start: 0.7753 (mttt) cc_final: 0.6696 (tptp) REVERT: D 214 CYS cc_start: 0.8019 (t) cc_final: 0.7640 (t) REVERT: E 178 LYS cc_start: 0.7151 (mttt) cc_final: 0.6462 (tptp) REVERT: E 214 CYS cc_start: 0.7770 (t) cc_final: 0.7523 (t) REVERT: F 178 LYS cc_start: 0.7564 (mttt) cc_final: 0.6841 (tptp) REVERT: G 145 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7351 (t0) REVERT: H 135 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: H 145 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7387 (t0) REVERT: H 178 LYS cc_start: 0.7672 (mttt) cc_final: 0.6804 (tptp) REVERT: H 192 MET cc_start: 0.7541 (mmt) cc_final: 0.7197 (mmt) REVERT: H 228 MET cc_start: 0.8228 (tpp) cc_final: 0.7872 (tpp) REVERT: I 145 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7128 (t0) REVERT: J 145 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7352 (t0) REVERT: J 178 LYS cc_start: 0.7525 (mttt) cc_final: 0.6445 (tptp) outliers start: 76 outliers final: 65 residues processed: 191 average time/residue: 0.2097 time to fit residues: 62.0505 Evaluate side-chains 215 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 142 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 174 THR 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 160 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 208 SER 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 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 135 TYR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR 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 E residue 235 THR Chi-restraints excluded: chain F residue 144 LEU 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 216 LEU 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 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 174 THR Chi-restraints excluded: chain I residue 182 ASN 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 163 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** C 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 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11600 Z= 0.215 Angle : 0.713 8.596 15770 Z= 0.386 Chirality : 0.059 0.414 2010 Planarity : 0.003 0.025 1900 Dihedral : 8.912 101.528 2330 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 5.56 % Allowed : 17.38 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 239 PHE 0.016 0.003 PHE B 237 TYR 0.020 0.002 TYR H 248 ARG 0.001 0.000 ARG J 140 ********************** 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 222 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 152 time to evaluate : 1.141 Fit side-chains REVERT: A 135 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.4944 (m-80) REVERT: A 145 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7338 (t0) REVERT: A 150 LEU cc_start: 0.8312 (mp) cc_final: 0.8104 (mp) REVERT: B 145 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 228 MET cc_start: 0.7649 (tpp) cc_final: 0.7148 (mmm) REVERT: C 178 LYS cc_start: 0.7736 (mttt) cc_final: 0.6703 (tptp) REVERT: C 216 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8109 (pp) REVERT: D 214 CYS cc_start: 0.8008 (t) cc_final: 0.7622 (t) REVERT: E 178 LYS cc_start: 0.7257 (mttt) cc_final: 0.6334 (tptp) REVERT: E 214 CYS cc_start: 0.7769 (t) cc_final: 0.7516 (t) REVERT: F 178 LYS cc_start: 0.7605 (mttt) cc_final: 0.6753 (tptp) REVERT: G 145 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7199 (t0) REVERT: H 145 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (t0) REVERT: H 228 MET cc_start: 0.8202 (tpp) cc_final: 0.7895 (tpp) REVERT: I 145 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7079 (t0) REVERT: J 145 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7280 (t0) outliers start: 70 outliers final: 60 residues processed: 191 average time/residue: 0.2098 time to fit residues: 63.0993 Evaluate side-chains 216 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 148 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 160 VAL Chi-restraints excluded: chain A residue 174 THR 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 145 ASN 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 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 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 144 LEU Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 174 THR 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 E residue 235 THR Chi-restraints excluded: chain F residue 144 LEU 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 216 LEU 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 207 MET 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 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 174 THR Chi-restraints excluded: chain I residue 182 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 40.0000 chunk 95 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** C 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5623 r_free = 0.5623 target = 0.383993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.353066 restraints weight = 12439.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5719 r_free = 0.5719 target = 0.350550 restraints weight = 19681.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5729 r_free = 0.5729 target = 0.348795 restraints weight = 17187.251| |-----------------------------------------------------------------------------| r_work (final): 0.5509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11600 Z= 0.336 Angle : 0.808 8.478 15770 Z= 0.442 Chirality : 0.062 0.437 2010 Planarity : 0.004 0.028 1900 Dihedral : 9.463 103.543 2330 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 6.11 % Allowed : 16.98 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.19), residues: 1330 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS B 239 PHE 0.017 0.004 PHE I 213 TYR 0.032 0.003 TYR H 248 ARG 0.001 0.000 ARG D 247 =============================================================================== Job complete usr+sys time: 1883.98 seconds wall clock time: 36 minutes 33.30 seconds (2193.30 seconds total)