Starting phenix.real_space_refine on Thu Mar 6 01:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.map" model { file = "/net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otd_17175/03_2025/8otd_17175.cif" } resolution = 2.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 28 5.16 5 C 2772 2.51 5 N 692 2.21 5 O 848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B, D Time building chain proxies: 3.55, per 1000 atoms: 0.82 Number of scatterers: 4340 At special positions: 0 Unit cell: (100.528, 97.232, 37.08, 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 28 16.00 O 848 8.00 N 692 7.00 C 2772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.07 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.07 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.07 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 253 " distance=2.07 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 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 520.4 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 68.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.034A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B 125 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 removed outlier: 6.477A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS B 129 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.868A pdb=" N VAL A 133 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 153 removed outlier: 6.874A pdb=" N ILE C 146 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 147 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN C 148 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 149 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU C 150 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 151 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 152 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 153 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG A 140 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR B 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 142 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN B 145 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 144 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR B 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ILE A 146 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N THR B 149 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASN A 148 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N ASN B 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LEU A 150 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N THR B 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE A 152 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG B 140 " --> pdb=" O THR D 141 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR D 143 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 142 " --> pdb=" O TYR D 143 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASN D 145 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU B 144 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR D 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ILE B 146 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N THR D 149 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASN B 148 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N ASN D 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LEU B 150 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N THR D 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE B 152 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 176 removed outlier: 6.751A pdb=" N VAL A 162 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU C 163 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 164 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 165 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A 166 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL B 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU A 161 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ASN B 164 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU A 163 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N THR B 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 165 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLN B 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 167 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN B 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 169 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER B 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 171 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR B 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS A 173 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE B 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 175 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR B 157 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL D 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 159 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL D 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU B 161 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ASN D 164 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU B 163 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N THR D 166 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 165 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLN D 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA B 167 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLN D 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 169 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER D 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE B 171 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR D 174 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS B 173 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE D 176 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 175 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 187 removed outlier: 8.672A pdb=" N ARG A 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N ASN C 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASN A 182 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER C 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 184 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 181 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 182 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A 183 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 181 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN D 182 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B 183 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 198 removed outlier: 5.862A pdb=" N LYS A 193 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP C 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 195 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N THR C 198 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR A 197 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 193 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN A 194 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS D 193 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 194 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 201 through 206 removed outlier: 6.552A pdb=" N THR A 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA C 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 203 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLU C 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 219 removed outlier: 6.838A pdb=" N THR C 215 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 216 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 217 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER A 218 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 219 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS B 214 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE A 213 " --> pdb=" O CYS B 214 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 216 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 215 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N SER B 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ILE A 217 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 209 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP D 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR B 211 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS D 214 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE B 213 " --> pdb=" O CYS D 214 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU D 216 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR B 215 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N SER D 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ILE B 217 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 230 removed outlier: 6.224A pdb=" N ASN A 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 226 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET C 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET A 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 230 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN A 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN B 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 230 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN D 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL B 230 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 233 through 252 removed outlier: 6.672A pdb=" N THR A 233 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR C 236 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 235 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY C 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE A 237 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER C 240 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS A 239 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLN C 242 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 241 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER C 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 243 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN A 245 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR C 248 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG A 247 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR C 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N GLN A 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP C 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 251 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP A 252 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 251 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASP B 252 " --> pdb=" O VAL D 251 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1058 1.34 - 1.46: 1274 1.46 - 1.58: 2032 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 4412 Sorted by residual: bond pdb=" CG HIS B 239 " pdb=" CD2 HIS B 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 6.20e+00 bond pdb=" CG HIS C 239 " pdb=" CD2 HIS C 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 6.03e+00 bond pdb=" CG HIS D 239 " pdb=" CD2 HIS D 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 5.97e+00 bond pdb=" CG HIS A 239 " pdb=" CD2 HIS A 239 " ideal model delta sigma weight residual 1.354 1.327 0.027 1.10e-02 8.26e+03 5.85e+00 bond pdb=" CA SER B 218 " pdb=" CB SER B 218 " ideal model delta sigma weight residual 1.530 1.497 0.034 1.50e-02 4.44e+03 5.06e+00 ... (remaining 4407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4616 1.56 - 3.11: 1091 3.11 - 4.67: 213 4.67 - 6.22: 60 6.22 - 7.78: 16 Bond angle restraints: 5996 Sorted by residual: angle pdb=" C ASP B 136 " pdb=" CA ASP B 136 " pdb=" CB ASP B 136 " ideal model delta sigma weight residual 109.84 117.62 -7.78 1.63e+00 3.76e-01 2.28e+01 angle pdb=" C ASP A 136 " pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " ideal model delta sigma weight residual 109.84 117.61 -7.77 1.63e+00 3.76e-01 2.27e+01 angle pdb=" C ASP D 136 " pdb=" CA ASP D 136 " pdb=" CB ASP D 136 " ideal model delta sigma weight residual 109.84 117.58 -7.74 1.63e+00 3.76e-01 2.26e+01 angle pdb=" C ASP C 136 " pdb=" CA ASP C 136 " pdb=" CB ASP C 136 " ideal model delta sigma weight residual 109.84 117.58 -7.74 1.63e+00 3.76e-01 2.25e+01 angle pdb=" N GLU D 246 " pdb=" CA GLU D 246 " pdb=" C GLU D 246 " ideal model delta sigma weight residual 108.76 116.05 -7.29 1.58e+00 4.01e-01 2.13e+01 ... (remaining 5991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 2256 14.88 - 29.77: 280 29.77 - 44.65: 60 44.65 - 59.54: 48 59.54 - 74.42: 16 Dihedral angle restraints: 2660 sinusoidal: 1036 harmonic: 1624 Sorted by residual: dihedral pdb=" CA THR C 231 " pdb=" C THR C 231 " pdb=" N VAL C 232 " pdb=" CA VAL C 232 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA THR A 231 " pdb=" C THR A 231 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA THR D 231 " pdb=" C THR D 231 " pdb=" N VAL D 232 " pdb=" CA VAL D 232 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 2657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 338 0.066 - 0.133: 270 0.133 - 0.199: 93 0.199 - 0.265: 7 0.265 - 0.331: 12 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS B 124 " pdb=" N LYS B 124 " pdb=" C LYS B 124 " pdb=" CB LYS B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS D 124 " pdb=" N LYS D 124 " pdb=" C LYS D 124 " pdb=" CB LYS D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS A 124 " pdb=" N LYS A 124 " pdb=" C LYS A 124 " pdb=" CB LYS A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 717 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 248 " 0.073 2.00e-02 2.50e+03 3.84e-02 2.95e+01 pdb=" CG TYR C 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR C 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 248 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 248 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 248 " 0.073 2.00e-02 2.50e+03 3.83e-02 2.94e+01 pdb=" CG TYR A 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR A 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 248 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 248 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 248 " 0.073 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR B 248 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 248 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 248 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 248 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 248 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 248 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 248 " 0.020 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 1994 2.96 - 3.45: 4022 3.45 - 3.93: 7646 3.93 - 4.42: 8118 4.42 - 4.90: 15622 Nonbonded interactions: 37402 Sorted by model distance: nonbonded pdb=" NZ LYS D 129 " pdb=" OD2 ASP D 136 " model vdw 2.478 3.120 nonbonded pdb=" NZ LYS A 129 " pdb=" OD2 ASP A 136 " model vdw 2.478 3.120 nonbonded pdb=" NZ LYS B 129 " pdb=" OD2 ASP B 136 " model vdw 2.478 3.120 nonbonded pdb=" NZ LYS C 129 " pdb=" OD2 ASP C 136 " model vdw 2.478 3.120 nonbonded pdb=" OG SER C 134 " pdb=" OD1 ASP C 136 " model vdw 2.504 3.040 ... (remaining 37397 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.008 0.043 4412 Z= 0.536 Angle : 1.482 7.777 5996 Z= 0.940 Chirality : 0.099 0.331 720 Planarity : 0.015 0.168 744 Dihedral : 16.818 74.422 1608 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.76 % Allowed : 5.56 % Favored : 89.68 % Cbeta Deviations : 0.77 % 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: -3.89 (0.27), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 239 PHE 0.017 0.006 PHE B 171 TYR 0.073 0.008 TYR C 248 ARG 0.026 0.005 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.455 Fit side-chains REVERT: A 178 LYS cc_start: 0.8086 (pttt) cc_final: 0.7376 (tttt) REVERT: B 172 SER cc_start: 0.8563 (t) cc_final: 0.8212 (m) REVERT: B 178 LYS cc_start: 0.8070 (pttt) cc_final: 0.7326 (tttt) REVERT: B 207 MET cc_start: 0.8322 (mtt) cc_final: 0.8079 (mtm) REVERT: C 145 ASN cc_start: 0.7983 (m-40) cc_final: 0.7709 (m-40) REVERT: C 178 LYS cc_start: 0.8235 (pttt) cc_final: 0.7533 (tttt) REVERT: C 247 ARG cc_start: 0.8300 (ttp80) cc_final: 0.6725 (ttp80) REVERT: D 172 SER cc_start: 0.8571 (t) cc_final: 0.8214 (m) REVERT: D 178 LYS cc_start: 0.8213 (pttt) cc_final: 0.7463 (tttt) outliers start: 24 outliers final: 0 residues processed: 159 average time/residue: 1.1475 time to fit residues: 188.7465 Evaluate side-chains 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 ASN A 151 ASN A 170 GLN A 182 ASN A 242 GLN B 145 ASN B 151 ASN B 156 ASN B 170 GLN B 182 ASN B 239 HIS B 242 GLN C 151 ASN C 170 GLN C 182 ASN C 242 GLN D 151 ASN D 170 GLN D 182 ASN D 239 HIS D 242 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.137180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.121569 restraints weight = 5069.161| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.75 r_work: 0.4002 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4412 Z= 0.248 Angle : 0.668 7.196 5996 Z= 0.369 Chirality : 0.053 0.142 720 Planarity : 0.003 0.028 744 Dihedral : 6.488 20.787 596 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.58 % Allowed : 17.26 % Favored : 80.16 % 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: -3.36 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 239 PHE 0.012 0.002 PHE B 213 TYR 0.022 0.002 TYR C 143 ARG 0.001 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.493 Fit side-chains REVERT: A 178 LYS cc_start: 0.7642 (pttt) cc_final: 0.6905 (ttmt) REVERT: A 207 MET cc_start: 0.8207 (mtp) cc_final: 0.7812 (mtt) REVERT: B 129 LYS cc_start: 0.7862 (pttt) cc_final: 0.7591 (pttp) REVERT: B 178 LYS cc_start: 0.7709 (pttt) cc_final: 0.6982 (ttpt) REVERT: C 178 LYS cc_start: 0.7828 (pttt) cc_final: 0.7011 (ttmt) REVERT: C 207 MET cc_start: 0.8486 (mtp) cc_final: 0.8133 (mtt) REVERT: D 172 SER cc_start: 0.8626 (t) cc_final: 0.8262 (m) REVERT: D 178 LYS cc_start: 0.7852 (pttt) cc_final: 0.7247 (tttt) outliers start: 13 outliers final: 4 residues processed: 125 average time/residue: 1.4198 time to fit residues: 182.6473 Evaluate side-chains 103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.0470 chunk 32 optimal weight: 0.5980 overall best weight: 1.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 ASN A 151 ASN B 151 ASN C 168 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.138767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.123249 restraints weight = 4790.522| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.70 r_work: 0.4010 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4412 Z= 0.217 Angle : 0.650 7.754 5996 Z= 0.350 Chirality : 0.053 0.135 720 Planarity : 0.003 0.024 744 Dihedral : 6.040 19.058 596 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.27 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 239 PHE 0.022 0.002 PHE D 213 TYR 0.021 0.002 TYR C 143 ARG 0.002 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.548 Fit side-chains REVERT: A 136 ASP cc_start: 0.8823 (p0) cc_final: 0.8497 (p0) REVERT: A 145 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7683 (m110) REVERT: A 178 LYS cc_start: 0.7706 (pttt) cc_final: 0.7054 (ttmt) REVERT: A 207 MET cc_start: 0.8190 (mtp) cc_final: 0.7819 (mtt) REVERT: B 163 GLU cc_start: 0.7343 (mp0) cc_final: 0.7127 (mp0) REVERT: B 178 LYS cc_start: 0.7719 (pttt) cc_final: 0.7045 (tttt) REVERT: C 178 LYS cc_start: 0.7832 (pttt) cc_final: 0.7031 (tttt) REVERT: C 180 ARG cc_start: 0.7706 (mtp180) cc_final: 0.6776 (mtt180) REVERT: C 207 MET cc_start: 0.8503 (mtp) cc_final: 0.8175 (mtt) REVERT: C 246 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: D 172 SER cc_start: 0.8612 (t) cc_final: 0.8245 (m) REVERT: D 178 LYS cc_start: 0.7903 (pttt) cc_final: 0.7289 (tttt) outliers start: 14 outliers final: 4 residues processed: 116 average time/residue: 1.4716 time to fit residues: 175.5530 Evaluate side-chains 104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 ASN A 151 ASN B 138 GLN D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.134784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.119230 restraints weight = 5111.244| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.73 r_work: 0.4026 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4412 Z= 0.229 Angle : 0.646 7.410 5996 Z= 0.348 Chirality : 0.052 0.132 720 Planarity : 0.003 0.022 744 Dihedral : 5.891 18.455 596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % 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: -3.14 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 239 PHE 0.023 0.002 PHE B 213 TYR 0.020 0.002 TYR A 248 ARG 0.003 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.7725 (pttt) cc_final: 0.7111 (ttmt) REVERT: A 192 MET cc_start: 0.7661 (mpp) cc_final: 0.7252 (mtp) REVERT: A 207 MET cc_start: 0.8176 (mtp) cc_final: 0.7807 (mtt) REVERT: B 178 LYS cc_start: 0.7704 (pttt) cc_final: 0.7092 (tttt) REVERT: C 178 LYS cc_start: 0.7873 (pttt) cc_final: 0.7067 (tttt) REVERT: C 207 MET cc_start: 0.8501 (mtp) cc_final: 0.8148 (mtt) REVERT: C 246 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: D 172 SER cc_start: 0.8655 (t) cc_final: 0.8272 (m) REVERT: D 178 LYS cc_start: 0.7860 (pttt) cc_final: 0.7276 (tttt) outliers start: 18 outliers final: 10 residues processed: 119 average time/residue: 1.4007 time to fit residues: 171.5988 Evaluate side-chains 109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 145 ASN A 151 ASN B 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.113252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.097596 restraints weight = 5706.365| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.75 r_work: 0.3820 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4412 Z= 0.421 Angle : 0.751 7.404 5996 Z= 0.405 Chirality : 0.055 0.134 720 Planarity : 0.003 0.021 744 Dihedral : 6.276 18.990 596 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.97 % Allowed : 18.65 % Favored : 77.38 % 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: -3.10 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.020 0.003 PHE A 213 TYR 0.030 0.003 TYR A 248 ARG 0.003 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.7798 (pttt) cc_final: 0.7184 (tttt) REVERT: A 192 MET cc_start: 0.7988 (mpp) cc_final: 0.7401 (mtp) REVERT: A 207 MET cc_start: 0.8383 (mtp) cc_final: 0.8004 (mtt) REVERT: B 122 ASP cc_start: 0.8830 (t70) cc_final: 0.8558 (t0) REVERT: B 178 LYS cc_start: 0.7668 (pttt) cc_final: 0.7139 (tttt) REVERT: C 178 LYS cc_start: 0.7959 (pttt) cc_final: 0.7186 (tttt) REVERT: D 178 LYS cc_start: 0.7860 (pttt) cc_final: 0.7269 (tttt) outliers start: 20 outliers final: 11 residues processed: 117 average time/residue: 1.3539 time to fit residues: 163.3253 Evaluate side-chains 103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 138 GLN C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.131436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.116264 restraints weight = 5202.545| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.69 r_work: 0.4010 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4412 Z= 0.264 Angle : 0.675 7.764 5996 Z= 0.360 Chirality : 0.053 0.129 720 Planarity : 0.003 0.018 744 Dihedral : 5.977 18.995 596 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.37 % Allowed : 19.25 % Favored : 77.38 % 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 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.020 0.003 PHE D 213 TYR 0.021 0.002 TYR A 248 ARG 0.003 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.7831 (pttt) cc_final: 0.7173 (tttt) REVERT: A 192 MET cc_start: 0.7826 (mpp) cc_final: 0.7427 (mtp) REVERT: A 207 MET cc_start: 0.8297 (mtp) cc_final: 0.7897 (mtt) REVERT: B 178 LYS cc_start: 0.7647 (pttt) cc_final: 0.7093 (ttmt) REVERT: C 178 LYS cc_start: 0.7912 (pttt) cc_final: 0.7108 (tttt) REVERT: D 178 LYS cc_start: 0.7925 (pttt) cc_final: 0.7264 (tttt) REVERT: D 207 MET cc_start: 0.8543 (mtt) cc_final: 0.8327 (mtp) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 1.4306 time to fit residues: 176.6465 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 151 ASN B 138 GLN C 138 GLN D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.112172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.096550 restraints weight = 5689.041| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.73 r_work: 0.3801 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 4412 Z= 0.493 Angle : 0.797 7.815 5996 Z= 0.427 Chirality : 0.056 0.133 720 Planarity : 0.003 0.022 744 Dihedral : 6.329 18.248 596 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.76 % Allowed : 18.65 % Favored : 76.59 % 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: -3.13 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.033 0.003 PHE A 213 TYR 0.033 0.003 TYR A 248 ARG 0.003 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8511 (t0) REVERT: A 178 LYS cc_start: 0.7786 (pttt) cc_final: 0.7141 (tttt) REVERT: A 183 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7602 (m-40) REVERT: A 192 MET cc_start: 0.7947 (mpp) cc_final: 0.7379 (mtp) REVERT: B 122 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8530 (t70) REVERT: B 178 LYS cc_start: 0.7640 (pttt) cc_final: 0.7098 (tttt) REVERT: C 178 LYS cc_start: 0.7865 (pttt) cc_final: 0.7100 (tttt) REVERT: D 124 LYS cc_start: 0.8772 (ptpp) cc_final: 0.8568 (ptpp) REVERT: D 178 LYS cc_start: 0.7863 (pttt) cc_final: 0.7262 (tttt) REVERT: D 207 MET cc_start: 0.8617 (mtt) cc_final: 0.8402 (mtp) outliers start: 24 outliers final: 13 residues processed: 120 average time/residue: 1.8532 time to fit residues: 230.2951 Evaluate side-chains 115 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 229 GLN B 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.137284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.122389 restraints weight = 5074.877| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.67 r_work: 0.4040 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4412 Z= 0.173 Angle : 0.649 10.769 5996 Z= 0.338 Chirality : 0.052 0.130 720 Planarity : 0.002 0.019 744 Dihedral : 5.637 17.237 596 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.98 % Allowed : 20.63 % Favored : 76.39 % 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: -3.06 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.020 0.002 PHE D 213 TYR 0.016 0.002 TYR C 143 ARG 0.003 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 178 LYS cc_start: 0.7764 (pttt) cc_final: 0.7108 (ttmt) REVERT: A 192 MET cc_start: 0.7808 (mpp) cc_final: 0.7226 (mtp) REVERT: A 207 MET cc_start: 0.8261 (mtp) cc_final: 0.7872 (mtt) REVERT: B 178 LYS cc_start: 0.7657 (pttt) cc_final: 0.7138 (ttmt) REVERT: C 178 LYS cc_start: 0.7822 (pttt) cc_final: 0.7001 (tttt) REVERT: D 178 LYS cc_start: 0.7890 (pttt) cc_final: 0.7278 (tttt) REVERT: D 213 PHE cc_start: 0.8090 (t80) cc_final: 0.7659 (t80) outliers start: 15 outliers final: 6 residues processed: 122 average time/residue: 1.7413 time to fit residues: 219.5501 Evaluate side-chains 109 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 151 ASN A 229 GLN B 138 GLN C 151 ASN C 168 GLN D 229 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.113475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.097700 restraints weight = 5711.334| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.74 r_work: 0.3817 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4412 Z= 0.411 Angle : 0.769 10.863 5996 Z= 0.409 Chirality : 0.055 0.131 720 Planarity : 0.003 0.042 744 Dihedral : 6.104 17.827 596 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.17 % Allowed : 21.63 % Favored : 75.20 % 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: -3.13 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.021 0.003 PHE B 213 TYR 0.028 0.003 TYR A 248 ARG 0.007 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7596 (m-40) REVERT: A 178 LYS cc_start: 0.7766 (pttt) cc_final: 0.7057 (tttt) REVERT: A 183 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7582 (m-40) REVERT: A 192 MET cc_start: 0.7956 (mpp) cc_final: 0.7375 (mtp) REVERT: B 149 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8332 (p) REVERT: B 178 LYS cc_start: 0.7594 (pttt) cc_final: 0.7077 (ttmt) REVERT: C 178 LYS cc_start: 0.7802 (pttt) cc_final: 0.7042 (tttt) REVERT: C 180 ARG cc_start: 0.7533 (mtp180) cc_final: 0.6745 (mtt180) REVERT: D 178 LYS cc_start: 0.7840 (pttt) cc_final: 0.7269 (tttt) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 1.6195 time to fit residues: 193.5533 Evaluate side-chains 111 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 253 CYS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 151 ASN A 229 GLN B 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.134720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.119259 restraints weight = 5043.425| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.76 r_work: 0.4043 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4412 Z= 0.209 Angle : 0.696 10.821 5996 Z= 0.360 Chirality : 0.052 0.128 720 Planarity : 0.003 0.038 744 Dihedral : 5.737 16.900 596 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.38 % Allowed : 21.83 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.13 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.018 0.002 PHE B 213 TYR 0.018 0.002 TYR C 143 ARG 0.008 0.001 ARG D 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 178 LYS cc_start: 0.7770 (pttt) cc_final: 0.7093 (ttmt) REVERT: A 192 MET cc_start: 0.7762 (mpp) cc_final: 0.7364 (mtp) REVERT: B 178 LYS cc_start: 0.7686 (pttt) cc_final: 0.7120 (ttmt) REVERT: C 178 LYS cc_start: 0.7762 (pttt) cc_final: 0.6961 (tttt) REVERT: D 124 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8289 (ptpp) REVERT: D 178 LYS cc_start: 0.7897 (pttt) cc_final: 0.7289 (tttt) REVERT: D 213 PHE cc_start: 0.8260 (t80) cc_final: 0.7838 (t80) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 1.4146 time to fit residues: 167.4665 Evaluate side-chains 107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 253 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 0.0470 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 2.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 151 ASN A 229 GLN B 138 GLN C 151 ASN D 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.133548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.118179 restraints weight = 5186.503| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.72 r_work: 0.4026 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4412 Z= 0.246 Angle : 0.713 11.151 5996 Z= 0.371 Chirality : 0.052 0.127 720 Planarity : 0.003 0.041 744 Dihedral : 5.746 17.042 596 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % Favored : 75.00 % 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: -3.11 (0.30), residues: 532 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 239 PHE 0.016 0.002 PHE B 213 TYR 0.019 0.002 TYR A 248 ARG 0.009 0.001 ARG D 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.02 seconds wall clock time: 83 minutes 12.07 seconds (4992.07 seconds total)