Starting phenix.real_space_refine on Wed Mar 4 04:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqt_71790/03_2026/9pqt_71790.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 1.000 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 5 5.21 5 S 30 5.16 5 C 6756 2.51 5 N 1758 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10487 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.21 Number of scatterers: 10487 At special positions: 0 Unit cell: (115.24, 122.98, 89.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 12 15.00 Mg 5 11.99 O 1926 8.00 N 1758 7.00 C 6756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.77 Conformation dependent library (CDL) restraints added in 529.5 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 17 sheets defined 46.9% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.908A pdb=" N ILE A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.501A pdb=" N LEU A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.613A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.693A pdb=" N ASN A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.663A pdb=" N MET A 227 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 228 " --> pdb=" O LYS A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 228' Processing helix chain 'A' and resid 230 through 238 removed outlier: 4.189A pdb=" N LEU A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.729A pdb=" N PHE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.516A pdb=" N LEU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.749A pdb=" N LEU A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.558A pdb=" N GLU B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.772A pdb=" N MET B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.535A pdb=" N ILE B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.560A pdb=" N ALA B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.794A pdb=" N LEU B 228 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.299A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.740A pdb=" N PHE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.543A pdb=" N LEU B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 removed outlier: 3.596A pdb=" N GLU C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.975A pdb=" N MET C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.702A pdb=" N ILE C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.637A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 238 removed outlier: 4.004A pdb=" N LEU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 removed outlier: 3.763A pdb=" N PHE C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 307 through 323 removed outlier: 3.527A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 removed outlier: 3.557A pdb=" N GLU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.650A pdb=" N LEU D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 162 removed outlier: 3.613A pdb=" N ASN D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.031A pdb=" N ILE D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.919A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 307 through 323 removed outlier: 3.747A pdb=" N LEU D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.742A pdb=" N ALA E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 removed outlier: 3.691A pdb=" N MET E 139 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.679A pdb=" N LYS E 153 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.568A pdb=" N ILE E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 removed outlier: 3.758A pdb=" N LEU E 228 " --> pdb=" O LYS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 239 removed outlier: 4.401A pdb=" N LEU E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 3.704A pdb=" N PHE E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 307 through 323 removed outlier: 3.837A pdb=" N ILE E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.541A pdb=" N ALA F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.544A pdb=" N LEU F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 162 removed outlier: 3.729A pdb=" N ILE F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.683A pdb=" N ASN F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.972A pdb=" N LEU F 228 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 239 removed outlier: 4.256A pdb=" N LEU F 234 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 3.579A pdb=" N PHE F 271 " --> pdb=" O PRO F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 307 through 322 removed outlier: 3.620A pdb=" N LEU F 312 " --> pdb=" O ASN F 308 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.159A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASP A 221 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA A 218 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR A 262 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 220 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR A 302 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TRP A 174 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 247 removed outlier: 3.881A pdb=" N LEU A 243 " --> pdb=" O TRP A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 274 removed outlier: 3.901A pdb=" N TRP A 273 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 281 " --> pdb=" O TRP A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.179A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP B 221 " --> pdb=" O TRP B 200 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA B 218 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR B 262 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE B 220 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 177 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 243 through 247 removed outlier: 3.814A pdb=" N LEU B 243 " --> pdb=" O TRP B 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.593A pdb=" N TRP B 273 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 281 " --> pdb=" O TRP B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 294 through 295 removed outlier: 3.555A pdb=" N GLU B 298 " --> pdb=" O TYR B 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 199 through 201 removed outlier: 6.421A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP C 221 " --> pdb=" O TRP C 200 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA C 218 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR C 262 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 220 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 243 through 247 removed outlier: 3.849A pdb=" N LEU C 243 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 250 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 199 through 201 removed outlier: 5.856A pdb=" N TRP D 200 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP D 221 " --> pdb=" O TRP D 200 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D 218 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR D 262 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE D 220 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 171 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL D 261 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 173 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 243 through 247 removed outlier: 3.684A pdb=" N LEU D 243 " --> pdb=" O TRP D 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 294 through 295 removed outlier: 3.608A pdb=" N GLU D 298 " --> pdb=" O TYR D 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 199 through 201 removed outlier: 6.018A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 221 " --> pdb=" O TRP E 200 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TYR E 302 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP E 174 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 243 through 247 removed outlier: 4.331A pdb=" N LEU E 243 " --> pdb=" O TRP E 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 199 through 201 removed outlier: 5.842A pdb=" N TRP F 200 " --> pdb=" O ILE F 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 243 through 247 removed outlier: 4.172A pdb=" N LEU F 243 " --> pdb=" O TRP F 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 273 through 274 removed outlier: 4.233A pdb=" N TRP F 273 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 281 " --> pdb=" O TRP F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 366 hydrogen bonds defined for protein. 1074 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: 1.46 Time building geometry restraints manager: 1.04 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: 3184 1.34 - 1.45: 1599 1.45 - 1.57: 5873 1.57 - 1.69: 18 1.69 - 1.81: 60 Bond restraints: 10734 Sorted by residual: bond pdb=" N PHE D 251 " pdb=" CA PHE D 251 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.10e+00 bond pdb=" C PHE D 251 " pdb=" O PHE D 251 " ideal model delta sigma weight residual 1.235 1.251 -0.016 1.22e-02 6.72e+03 1.80e+00 bond pdb=" CG GLN B 272 " pdb=" CD GLN B 272 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" CA ASP B 297 " pdb=" CB ASP B 297 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.09e+00 bond pdb=" CG ARG E 213 " pdb=" CD ARG E 213 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 ... (remaining 10729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14110 1.64 - 3.29: 288 3.29 - 4.93: 85 4.93 - 6.58: 33 6.58 - 8.22: 4 Bond angle restraints: 14520 Sorted by residual: angle pdb=" CA ASP B 297 " pdb=" CB ASP B 297 " pdb=" CG ASP B 297 " ideal model delta sigma weight residual 112.60 114.97 -2.37 1.00e+00 1.00e+00 5.63e+00 angle pdb=" CA LEU C 243 " pdb=" CB LEU C 243 " pdb=" CG LEU C 243 " ideal model delta sigma weight residual 116.30 124.52 -8.22 3.50e+00 8.16e-02 5.52e+00 angle pdb=" CB GLU F 152 " pdb=" CG GLU F 152 " pdb=" CD GLU F 152 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.70e+00 3.46e-01 5.23e+00 angle pdb=" CG ARG E 213 " pdb=" CD ARG E 213 " pdb=" NE ARG E 213 " ideal model delta sigma weight residual 112.00 116.97 -4.97 2.20e+00 2.07e-01 5.11e+00 angle pdb=" CA LEU D 243 " pdb=" CB LEU D 243 " pdb=" CG LEU D 243 " ideal model delta sigma weight residual 116.30 124.03 -7.73 3.50e+00 8.16e-02 4.88e+00 ... (remaining 14515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 6078 31.26 - 62.53: 253 62.53 - 93.79: 30 93.79 - 125.06: 0 125.06 - 156.32: 5 Dihedral angle restraints: 6366 sinusoidal: 2772 harmonic: 3594 Sorted by residual: dihedral pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" N9 ADP D 401 " pdb=" C4 ADP D 401 " ideal model delta sinusoidal sigma weight residual 91.55 -64.78 156.32 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C2' ADP E 401 " pdb=" C1' ADP E 401 " pdb=" N9 ADP E 401 " pdb=" C4 ADP E 401 " ideal model delta sinusoidal sigma weight residual 91.55 -59.90 151.45 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C2' ADP A 401 " pdb=" C1' ADP A 401 " pdb=" N9 ADP A 401 " pdb=" C4 ADP A 401 " ideal model delta sinusoidal sigma weight residual 91.55 -56.95 148.49 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 6363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 957 0.029 - 0.059: 365 0.059 - 0.088: 87 0.088 - 0.117: 100 0.117 - 0.147: 15 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C2' ADP F 401 " pdb=" C1' ADP F 401 " pdb=" C3' ADP F 401 " pdb=" O2' ADP F 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" C3' ADP C 401 " pdb=" O2' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CB ILE D 244 " pdb=" CA ILE D 244 " pdb=" CG1 ILE D 244 " pdb=" CG2 ILE D 244 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1521 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 297 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ASP B 297 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP B 297 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 298 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 255 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 256 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 255 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 256 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.023 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 80 2.60 - 3.18: 8568 3.18 - 3.75: 14728 3.75 - 4.33: 20659 4.33 - 4.90: 34103 Nonbonded interactions: 78138 Sorted by model distance: nonbonded pdb=" OG1 THR C 184 " pdb="MG MG C 402 " model vdw 2.026 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.037 2.170 nonbonded pdb=" OG1 THR A 184 " pdb="MG MG A 402 " model vdw 2.040 2.170 nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR D 184 " pdb="MG MG D 402 " model vdw 2.059 2.170 ... (remaining 78133 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' and resid 121 through 401) selection = (chain 'B' and resid 121 through 401) selection = (chain 'C' and resid 121 through 401) selection = (chain 'D' and resid 121 through 401) selection = (chain 'E' and resid 121 through 401) selection = chain 'F' } 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: 2.170 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.002 0.031 10734 Z= 0.114 Angle : 0.651 8.222 14520 Z= 0.305 Chirality : 0.041 0.147 1524 Planarity : 0.004 0.054 1818 Dihedral : 17.076 156.323 4050 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1230 helix: 0.20 (0.23), residues: 462 sheet: 1.31 (0.38), residues: 192 loop : 0.16 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 213 TYR 0.022 0.001 TYR D 167 PHE 0.015 0.001 PHE A 233 TRP 0.023 0.002 TRP B 307 Details of bonding type rmsd covalent geometry : bond 0.00247 (10734) covalent geometry : angle 0.65131 (14520) hydrogen bonds : bond 0.30248 ( 366) hydrogen bonds : angle 8.17491 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 THR cc_start: 0.8195 (m) cc_final: 0.7994 (m) REVERT: B 284 ASP cc_start: 0.7986 (t0) cc_final: 0.7565 (p0) REVERT: C 196 ASN cc_start: 0.8091 (t0) cc_final: 0.7778 (t0) REVERT: C 199 TYR cc_start: 0.8409 (p90) cc_final: 0.8168 (p90) REVERT: C 201 MET cc_start: 0.8440 (mmm) cc_final: 0.8039 (mmt) REVERT: D 152 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7524 (tp30) REVERT: D 201 MET cc_start: 0.7871 (mmm) cc_final: 0.7464 (mmt) REVERT: D 312 LEU cc_start: 0.8088 (pp) cc_final: 0.7553 (mp) REVERT: D 321 TYR cc_start: 0.8219 (t80) cc_final: 0.7938 (t80) REVERT: E 181 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7741 (tp30) REVERT: E 201 MET cc_start: 0.8685 (mmm) cc_final: 0.8229 (mmt) REVERT: F 125 LYS cc_start: 0.8696 (mtmt) cc_final: 0.7735 (mmtt) REVERT: F 201 MET cc_start: 0.8476 (mmm) cc_final: 0.8076 (mmm) REVERT: F 280 ILE cc_start: 0.7228 (mm) cc_final: 0.6910 (tt) REVERT: F 319 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7238 (tpp80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0888 time to fit residues: 27.0739 Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 286 GLN C 272 GLN D 288 GLN F 133 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.113784 restraints weight = 15915.914| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.82 r_work: 0.3480 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10734 Z= 0.144 Angle : 0.660 6.628 14520 Z= 0.319 Chirality : 0.045 0.144 1524 Planarity : 0.004 0.032 1818 Dihedral : 10.634 156.150 1410 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.82 % Allowed : 11.08 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1230 helix: 0.69 (0.22), residues: 501 sheet: 1.31 (0.37), residues: 192 loop : -0.12 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 213 TYR 0.019 0.002 TYR F 321 PHE 0.015 0.001 PHE F 195 TRP 0.019 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00326 (10734) covalent geometry : angle 0.65984 (14520) hydrogen bonds : bond 0.05031 ( 366) hydrogen bonds : angle 5.57087 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 VAL cc_start: 0.8281 (t) cc_final: 0.8008 (t) REVERT: C 196 ASN cc_start: 0.8006 (t0) cc_final: 0.7591 (t0) REVERT: C 199 TYR cc_start: 0.8650 (p90) cc_final: 0.8447 (p90) REVERT: D 152 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7355 (tp30) REVERT: D 201 MET cc_start: 0.8021 (mmm) cc_final: 0.7483 (tpp) REVERT: D 312 LEU cc_start: 0.8447 (pp) cc_final: 0.7816 (mp) REVERT: D 321 TYR cc_start: 0.8454 (t80) cc_final: 0.8127 (t80) REVERT: E 201 MET cc_start: 0.8881 (mmm) cc_final: 0.8538 (mmt) REVERT: E 239 ASP cc_start: 0.8623 (t0) cc_final: 0.8385 (m-30) REVERT: F 125 LYS cc_start: 0.8799 (mtmt) cc_final: 0.7867 (mmtt) REVERT: F 193 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7042 (mtm110) REVERT: F 280 ILE cc_start: 0.7261 (mm) cc_final: 0.6967 (tt) REVERT: F 291 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8312 (ttm-80) REVERT: F 319 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7306 (tpp80) outliers start: 9 outliers final: 5 residues processed: 169 average time/residue: 0.1001 time to fit residues: 23.9607 Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 303 ASN C 303 ASN F 133 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113164 restraints weight = 16071.302| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.94 r_work: 0.3469 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10734 Z= 0.144 Angle : 0.629 6.453 14520 Z= 0.298 Chirality : 0.044 0.156 1524 Planarity : 0.004 0.031 1818 Dihedral : 10.611 155.788 1410 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.47 % Allowed : 12.45 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1230 helix: 0.93 (0.23), residues: 484 sheet: 1.11 (0.36), residues: 197 loop : -0.05 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.020 0.002 TYR E 321 PHE 0.010 0.001 PHE E 195 TRP 0.016 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00338 (10734) covalent geometry : angle 0.62925 (14520) hydrogen bonds : bond 0.04384 ( 366) hydrogen bonds : angle 5.14167 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7415 (t0) REVERT: C 160 VAL cc_start: 0.8497 (t) cc_final: 0.8249 (t) REVERT: C 192 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: C 196 ASN cc_start: 0.7957 (t0) cc_final: 0.7485 (t0) REVERT: C 201 MET cc_start: 0.8657 (mmm) cc_final: 0.8300 (mtp) REVERT: C 243 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7608 (tt) REVERT: D 152 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7451 (tp30) REVERT: D 189 ASP cc_start: 0.7610 (p0) cc_final: 0.7405 (p0) REVERT: D 201 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: D 321 TYR cc_start: 0.8463 (t80) cc_final: 0.8227 (t80) REVERT: E 201 MET cc_start: 0.8908 (mmm) cc_final: 0.8560 (mmm) REVERT: E 239 ASP cc_start: 0.8648 (t0) cc_final: 0.8397 (m-30) REVERT: F 125 LYS cc_start: 0.8743 (mtmt) cc_final: 0.7744 (mmtt) REVERT: F 280 ILE cc_start: 0.7303 (mm) cc_final: 0.7016 (tt) outliers start: 16 outliers final: 9 residues processed: 170 average time/residue: 0.0939 time to fit residues: 22.7710 Evaluate side-chains 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 262 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN C 303 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113401 restraints weight = 16168.827| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.95 r_work: 0.3467 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10734 Z= 0.128 Angle : 0.614 10.193 14520 Z= 0.286 Chirality : 0.043 0.158 1524 Planarity : 0.003 0.032 1818 Dihedral : 10.533 155.213 1410 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.38 % Allowed : 12.73 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1230 helix: 0.95 (0.22), residues: 509 sheet: 0.97 (0.35), residues: 202 loop : -0.06 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 292 TYR 0.017 0.001 TYR E 321 PHE 0.008 0.001 PHE E 195 TRP 0.015 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00298 (10734) covalent geometry : angle 0.61397 (14520) hydrogen bonds : bond 0.03841 ( 366) hydrogen bonds : angle 4.94180 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 146 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6325 (tp) REVERT: C 160 VAL cc_start: 0.8495 (t) cc_final: 0.8254 (t) REVERT: C 196 ASN cc_start: 0.7996 (t0) cc_final: 0.7516 (t0) REVERT: C 243 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7614 (tt) REVERT: D 127 GLU cc_start: 0.8337 (pp20) cc_final: 0.8064 (pp20) REVERT: D 152 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7435 (tp30) REVERT: D 201 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: D 321 TYR cc_start: 0.8442 (t80) cc_final: 0.8213 (t80) REVERT: E 201 MET cc_start: 0.8918 (mmm) cc_final: 0.8593 (mmm) REVERT: E 239 ASP cc_start: 0.8671 (t0) cc_final: 0.8414 (m-30) REVERT: F 125 LYS cc_start: 0.8742 (mtmt) cc_final: 0.7736 (mmtt) REVERT: F 280 ILE cc_start: 0.7377 (mm) cc_final: 0.7122 (tt) outliers start: 26 outliers final: 16 residues processed: 162 average time/residue: 0.0803 time to fit residues: 19.4553 Evaluate side-chains 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 262 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 106 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.146625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115156 restraints weight = 16075.605| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.95 r_work: 0.3497 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10734 Z= 0.097 Angle : 0.590 10.604 14520 Z= 0.269 Chirality : 0.042 0.159 1524 Planarity : 0.003 0.031 1818 Dihedral : 10.379 154.384 1410 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.74 % Allowed : 14.01 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1230 helix: 1.14 (0.22), residues: 516 sheet: 0.95 (0.35), residues: 202 loop : -0.03 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.014 0.001 TYR E 321 PHE 0.008 0.001 PHE F 195 TRP 0.014 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00211 (10734) covalent geometry : angle 0.59037 (14520) hydrogen bonds : bond 0.03289 ( 366) hydrogen bonds : angle 4.74541 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 THR cc_start: 0.6176 (t) cc_final: 0.5878 (p) REVERT: C 160 VAL cc_start: 0.8500 (t) cc_final: 0.8267 (t) REVERT: C 196 ASN cc_start: 0.7943 (t0) cc_final: 0.7457 (t0) REVERT: C 243 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7558 (tt) REVERT: D 152 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7387 (tp30) REVERT: D 201 MET cc_start: 0.8199 (mmm) cc_final: 0.7977 (mmm) REVERT: D 321 TYR cc_start: 0.8413 (t80) cc_final: 0.8198 (t80) REVERT: E 201 MET cc_start: 0.8930 (mmm) cc_final: 0.8567 (mmm) REVERT: E 239 ASP cc_start: 0.8663 (t0) cc_final: 0.8402 (m-30) REVERT: F 125 LYS cc_start: 0.8738 (mtmt) cc_final: 0.7733 (mmtt) REVERT: F 280 ILE cc_start: 0.7305 (mm) cc_final: 0.7055 (tt) outliers start: 19 outliers final: 14 residues processed: 165 average time/residue: 0.0825 time to fit residues: 19.9658 Evaluate side-chains 164 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 229 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN E 131 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.147388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115886 restraints weight = 16082.904| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.97 r_work: 0.3508 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10734 Z= 0.095 Angle : 0.583 10.169 14520 Z= 0.264 Chirality : 0.042 0.164 1524 Planarity : 0.003 0.030 1818 Dihedral : 10.233 153.985 1410 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.92 % Allowed : 14.65 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1230 helix: 1.29 (0.22), residues: 517 sheet: 1.01 (0.35), residues: 202 loop : 0.01 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.014 0.001 TYR E 321 PHE 0.007 0.001 PHE F 138 TRP 0.013 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00206 (10734) covalent geometry : angle 0.58294 (14520) hydrogen bonds : bond 0.03118 ( 366) hydrogen bonds : angle 4.64096 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8496 (tptt) cc_final: 0.7772 (mptt) REVERT: A 146 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6425 (tp) REVERT: A 205 THR cc_start: 0.6143 (t) cc_final: 0.5878 (p) REVERT: C 196 ASN cc_start: 0.7916 (t0) cc_final: 0.7403 (t0) REVERT: C 201 MET cc_start: 0.8688 (mmm) cc_final: 0.8018 (mmt) REVERT: C 243 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7581 (tt) REVERT: D 152 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7279 (tp30) REVERT: D 196 ASN cc_start: 0.7552 (t0) cc_final: 0.7296 (t0) REVERT: D 201 MET cc_start: 0.8191 (mmm) cc_final: 0.7961 (mmm) REVERT: E 201 MET cc_start: 0.8935 (mmm) cc_final: 0.8638 (mmt) REVERT: E 239 ASP cc_start: 0.8651 (t0) cc_final: 0.8378 (m-30) REVERT: F 125 LYS cc_start: 0.8734 (mtmt) cc_final: 0.7730 (mmtt) REVERT: F 280 ILE cc_start: 0.7232 (mm) cc_final: 0.6992 (tt) outliers start: 21 outliers final: 16 residues processed: 172 average time/residue: 0.0858 time to fit residues: 21.2946 Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113500 restraints weight = 15690.311| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.79 r_work: 0.3480 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10734 Z= 0.131 Angle : 0.613 10.354 14520 Z= 0.284 Chirality : 0.043 0.173 1524 Planarity : 0.003 0.038 1818 Dihedral : 10.325 154.865 1410 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.92 % Allowed : 15.29 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1230 helix: 1.29 (0.23), residues: 509 sheet: 0.95 (0.34), residues: 206 loop : -0.09 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 292 TYR 0.016 0.001 TYR F 212 PHE 0.008 0.001 PHE C 271 TRP 0.013 0.001 TRP D 273 Details of bonding type rmsd covalent geometry : bond 0.00307 (10734) covalent geometry : angle 0.61333 (14520) hydrogen bonds : bond 0.03669 ( 366) hydrogen bonds : angle 4.72478 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8533 (tptt) cc_final: 0.7836 (mptt) REVERT: A 205 THR cc_start: 0.6207 (t) cc_final: 0.5856 (p) REVERT: C 192 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: C 196 ASN cc_start: 0.8035 (t0) cc_final: 0.7544 (t0) REVERT: C 243 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7650 (tt) REVERT: D 127 GLU cc_start: 0.8328 (pp20) cc_final: 0.8026 (pp20) REVERT: D 152 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7416 (tp30) REVERT: D 321 TYR cc_start: 0.8378 (t80) cc_final: 0.8075 (t80) REVERT: E 201 MET cc_start: 0.8862 (mmm) cc_final: 0.8575 (mmm) REVERT: E 239 ASP cc_start: 0.8641 (t0) cc_final: 0.8364 (m-30) REVERT: F 125 LYS cc_start: 0.8721 (mtmt) cc_final: 0.7712 (mmtt) REVERT: F 239 ASP cc_start: 0.8356 (t0) cc_final: 0.8069 (m-30) REVERT: F 280 ILE cc_start: 0.7383 (mm) cc_final: 0.7162 (tt) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.0883 time to fit residues: 21.2105 Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 262 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 272 GLN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.144716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114068 restraints weight = 15696.919| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.78 r_work: 0.3488 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10734 Z= 0.123 Angle : 0.611 9.818 14520 Z= 0.284 Chirality : 0.043 0.175 1524 Planarity : 0.003 0.038 1818 Dihedral : 10.302 154.506 1410 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.92 % Allowed : 15.48 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1230 helix: 1.22 (0.23), residues: 516 sheet: 0.92 (0.35), residues: 202 loop : -0.07 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 292 TYR 0.014 0.001 TYR E 321 PHE 0.008 0.001 PHE C 271 TRP 0.013 0.001 TRP E 254 Details of bonding type rmsd covalent geometry : bond 0.00285 (10734) covalent geometry : angle 0.61070 (14520) hydrogen bonds : bond 0.03517 ( 366) hydrogen bonds : angle 4.69617 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8515 (tptt) cc_final: 0.7805 (mptt) REVERT: A 205 THR cc_start: 0.6238 (t) cc_final: 0.5893 (p) REVERT: C 192 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: C 196 ASN cc_start: 0.7978 (t0) cc_final: 0.7474 (t0) REVERT: C 243 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7579 (tt) REVERT: D 152 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7394 (tp30) REVERT: D 196 ASN cc_start: 0.7559 (t0) cc_final: 0.7359 (t0) REVERT: D 201 MET cc_start: 0.8322 (mmm) cc_final: 0.7742 (tpp) REVERT: D 221 ASP cc_start: 0.8400 (m-30) cc_final: 0.7996 (m-30) REVERT: D 321 TYR cc_start: 0.8360 (t80) cc_final: 0.8076 (t80) REVERT: E 201 MET cc_start: 0.8890 (mmm) cc_final: 0.8572 (mmm) REVERT: E 239 ASP cc_start: 0.8623 (t0) cc_final: 0.8330 (m-30) REVERT: F 125 LYS cc_start: 0.8718 (mtmt) cc_final: 0.7704 (mmtt) REVERT: F 239 ASP cc_start: 0.8362 (t0) cc_final: 0.8066 (m-30) outliers start: 21 outliers final: 18 residues processed: 157 average time/residue: 0.0825 time to fit residues: 19.1341 Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 262 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** 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 = 0.4049 r_free = 0.4049 target = 0.146323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115545 restraints weight = 15661.827| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.81 r_work: 0.3506 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10734 Z= 0.103 Angle : 0.593 9.527 14520 Z= 0.273 Chirality : 0.042 0.175 1524 Planarity : 0.003 0.030 1818 Dihedral : 10.208 153.804 1410 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.83 % Allowed : 15.84 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.23), residues: 1230 helix: 1.28 (0.23), residues: 517 sheet: 0.92 (0.34), residues: 206 loop : -0.06 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 292 TYR 0.014 0.001 TYR E 321 PHE 0.007 0.001 PHE E 195 TRP 0.013 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00230 (10734) covalent geometry : angle 0.59332 (14520) hydrogen bonds : bond 0.03161 ( 366) hydrogen bonds : angle 4.61478 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8509 (tptt) cc_final: 0.7835 (mptt) REVERT: A 146 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6392 (tp) REVERT: A 198 GLU cc_start: 0.7667 (pt0) cc_final: 0.7254 (pm20) REVERT: A 205 THR cc_start: 0.6142 (t) cc_final: 0.5865 (p) REVERT: C 192 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: C 196 ASN cc_start: 0.7968 (t0) cc_final: 0.7446 (t0) REVERT: C 199 TYR cc_start: 0.8634 (p90) cc_final: 0.8257 (p90) REVERT: C 201 MET cc_start: 0.8640 (mmm) cc_final: 0.8150 (mmt) REVERT: C 243 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7442 (tt) REVERT: D 152 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7359 (tp30) REVERT: D 201 MET cc_start: 0.8230 (mmm) cc_final: 0.7711 (tpp) REVERT: D 221 ASP cc_start: 0.8372 (m-30) cc_final: 0.7924 (m-30) REVERT: D 321 TYR cc_start: 0.8299 (t80) cc_final: 0.8026 (t80) REVERT: E 201 MET cc_start: 0.8885 (mmm) cc_final: 0.8562 (mmm) REVERT: E 239 ASP cc_start: 0.8616 (t0) cc_final: 0.8351 (m-30) REVERT: F 125 LYS cc_start: 0.8694 (mtmt) cc_final: 0.7701 (mmtt) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.0904 time to fit residues: 20.9150 Evaluate side-chains 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 102 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.144239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.113431 restraints weight = 15647.665| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.80 r_work: 0.3476 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10734 Z= 0.136 Angle : 0.622 9.244 14520 Z= 0.291 Chirality : 0.043 0.179 1524 Planarity : 0.003 0.040 1818 Dihedral : 10.318 154.569 1410 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.83 % Allowed : 16.21 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1230 helix: 1.26 (0.23), residues: 510 sheet: 0.85 (0.34), residues: 206 loop : -0.12 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 292 TYR 0.014 0.002 TYR E 295 PHE 0.008 0.001 PHE C 271 TRP 0.013 0.001 TRP E 254 Details of bonding type rmsd covalent geometry : bond 0.00320 (10734) covalent geometry : angle 0.62199 (14520) hydrogen bonds : bond 0.03651 ( 366) hydrogen bonds : angle 4.72973 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7690 (pt0) cc_final: 0.7263 (pm20) REVERT: A 205 THR cc_start: 0.6245 (t) cc_final: 0.5897 (p) REVERT: C 192 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: C 196 ASN cc_start: 0.8009 (t0) cc_final: 0.7505 (t0) REVERT: C 243 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7663 (tt) REVERT: D 152 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7400 (tp30) REVERT: D 321 TYR cc_start: 0.8308 (t80) cc_final: 0.8011 (t80) REVERT: E 201 MET cc_start: 0.8847 (mmm) cc_final: 0.8576 (mmm) REVERT: E 239 ASP cc_start: 0.8630 (t0) cc_final: 0.8343 (m-30) REVERT: F 125 LYS cc_start: 0.8716 (mtmt) cc_final: 0.7721 (mmtt) REVERT: F 239 ASP cc_start: 0.8427 (t0) cc_final: 0.8145 (m-30) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.0934 time to fit residues: 21.1397 Evaluate side-chains 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 262 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.146747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115916 restraints weight = 15709.629| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.82 r_work: 0.3515 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10734 Z= 0.099 Angle : 0.600 9.223 14520 Z= 0.277 Chirality : 0.042 0.180 1524 Planarity : 0.003 0.031 1818 Dihedral : 10.107 153.544 1410 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 16.48 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1230 helix: 1.33 (0.23), residues: 517 sheet: 0.90 (0.34), residues: 206 loop : -0.09 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 292 TYR 0.014 0.001 TYR E 295 PHE 0.007 0.001 PHE E 195 TRP 0.014 0.001 TRP B 254 Details of bonding type rmsd covalent geometry : bond 0.00217 (10734) covalent geometry : angle 0.59976 (14520) hydrogen bonds : bond 0.03071 ( 366) hydrogen bonds : angle 4.60725 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.39 seconds wall clock time: 37 minutes 52.83 seconds (2272.83 seconds total)