Starting phenix.real_space_refine on Wed Mar 4 11:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe0_20320/03_2026/6pe0_20320_neut_trim.cif" } resolution = 3.5 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= 0.006 sd= 0.065 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 15 5.49 5 Mg 5 5.21 5 S 59 5.16 5 C 8268 2.51 5 N 2349 2.21 5 O 2490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s 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: 13186 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1914 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 15, 'TRANS': 232} Chain breaks: 1 Chain: "A" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2050 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 245} Chain breaks: 4 Chain: "B" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2209 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2293 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain breaks: 1 Chain: "E" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2183 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.34, per 1000 atoms: 0.25 Number of scatterers: 13186 At special positions: 0 Unit cell: (86.838, 139.788, 135.552, 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 59 16.00 P 15 15.00 Mg 5 11.99 O 2490 8.00 N 2349 7.00 C 8268 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: 1.10 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 7 sheets defined 51.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'F' and resid 92 through 98 removed outlier: 5.313A pdb=" N LEU F 98 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.530A pdb=" N LEU F 163 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA F 164 " --> pdb=" O LYS F 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 184 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.573A pdb=" N PHE F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 242 removed outlier: 3.715A pdb=" N MET F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP F 242 " --> pdb=" O MET F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 288 through 298 removed outlier: 3.626A pdb=" N ARG F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 removed outlier: 4.565A pdb=" N THR F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'A' and resid 49 through 64 Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.998A pdb=" N VAL A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 127 through 132 removed outlier: 4.095A pdb=" N LEU A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 214 through 219 removed outlier: 4.351A pdb=" N VAL A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.644A pdb=" N MET A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.929A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.813A pdb=" N ILE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 344 removed outlier: 3.700A pdb=" N LYS A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'B' and resid 45 through 65 removed outlier: 3.603A pdb=" N ILE B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.816A pdb=" N GLU B 99 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 127 through 132 removed outlier: 4.110A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.169A pdb=" N LYS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.905A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.746A pdb=" N ARG B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 4.132A pdb=" N ILE B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 removed outlier: 3.591A pdb=" N CYS B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 340 through 345 Processing helix chain 'C' and resid 45 through 64 removed outlier: 3.724A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.860A pdb=" N GLN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 96' Processing helix chain 'C' and resid 97 through 100 removed outlier: 3.599A pdb=" N VAL C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.769A pdb=" N ILE C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.738A pdb=" N ALA C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.508A pdb=" N ILE C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.889A pdb=" N VAL C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.618A pdb=" N ASP C 267 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 268 " --> pdb=" O ILE C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.972A pdb=" N ARG C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.605A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'D' and resid 43 through 64 removed outlier: 4.123A pdb=" N GLN D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.856A pdb=" N VAL D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.723A pdb=" N ASP D 112 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 113 " --> pdb=" O PHE D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 113' Processing helix chain 'D' and resid 116 through 125 removed outlier: 3.605A pdb=" N GLU D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.736A pdb=" N ALA D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.643A pdb=" N PHE D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 238 removed outlier: 3.858A pdb=" N PHE D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.664A pdb=" N GLU D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.573A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 341 Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 45 through 64 removed outlier: 4.452A pdb=" N GLN E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.727A pdb=" N LYS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 133 through 139 removed outlier: 3.794A pdb=" N LEU E 136 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.939A pdb=" N ALA E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 removed outlier: 3.672A pdb=" N LEU E 183 " --> pdb=" O HIS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.572A pdb=" N LYS E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 removed outlier: 4.319A pdb=" N VAL E 218 " --> pdb=" O GLN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 232 through 242 Processing helix chain 'E' and resid 286 through 298 removed outlier: 3.514A pdb=" N ARG E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 3.868A pdb=" N ILE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 332 Processing helix chain 'E' and resid 333 through 339 removed outlier: 4.091A pdb=" N GLU E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 339 " --> pdb=" O PRO E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing sheet with id=AA1, first strand: chain 'F' and resid 100 through 101 removed outlier: 6.932A pdb=" N ILE F 209 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY F 149 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE F 280 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 151 " --> pdb=" O PHE F 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.828A pdb=" N LEU A 151 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.798A pdb=" N SER A 174 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER A 208 " --> pdb=" O VAL A 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 178 removed outlier: 3.752A pdb=" N ILE B 209 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER B 208 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU B 259 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE B 210 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 175 through 177 removed outlier: 6.520A pdb=" N ILE C 176 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASP C 213 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 261 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 150 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS C 278 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 174 through 177 removed outlier: 6.353A pdb=" N SER D 174 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE D 211 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE D 176 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP D 213 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER D 208 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 259 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE D 210 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA D 261 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE D 212 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL D 150 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR D 262 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 152 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 176 through 177 removed outlier: 6.899A pdb=" N ILE E 176 " --> pdb=" O PHE E 211 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE E 210 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA E 261 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 212 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 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: 1.93 Time building geometry restraints manager: 1.37 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: 4244 1.34 - 1.45: 1441 1.45 - 1.57: 7592 1.57 - 1.69: 25 1.69 - 1.81: 106 Bond restraints: 13408 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.55e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.55e+01 ... (remaining 13403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 18058 4.57 - 9.14: 89 9.14 - 13.70: 5 13.70 - 18.27: 4 18.27 - 22.84: 6 Bond angle restraints: 18162 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 117.03 22.84 1.00e+00 1.00e+00 5.22e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 118.44 21.43 1.00e+00 1.00e+00 4.59e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 119.06 20.81 1.00e+00 1.00e+00 4.33e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.14 19.73 1.00e+00 1.00e+00 3.89e+02 ... (remaining 18157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 7765 16.56 - 33.13: 437 33.13 - 49.69: 112 49.69 - 66.26: 21 66.26 - 82.82: 9 Dihedral angle restraints: 8344 sinusoidal: 3552 harmonic: 4792 Sorted by residual: dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 134.48 45.52 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA GLN E 206 " pdb=" C GLN E 206 " pdb=" N PRO E 207 " pdb=" CA PRO E 207 " ideal model delta harmonic sigma weight residual 180.00 140.98 39.02 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" CA TYR B 129 " pdb=" C TYR B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 8341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1956 0.096 - 0.192: 98 0.192 - 0.288: 3 0.288 - 0.384: 2 0.384 - 0.480: 2 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA ALA A 229 " pdb=" N ALA A 229 " pdb=" C ALA A 229 " pdb=" CB ALA A 229 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 91 " pdb=" N GLU F 91 " pdb=" C GLU F 91 " pdb=" CB GLU F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA ILE A 215 " pdb=" N ILE A 215 " pdb=" C ILE A 215 " pdb=" CB ILE A 215 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2058 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 129 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO D 130 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 129 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO B 130 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 338 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLU B 338 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU B 338 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR B 339 " 0.020 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 59 2.36 - 3.00: 7369 3.00 - 3.63: 20603 3.63 - 4.27: 29602 4.27 - 4.90: 47792 Nonbonded interactions: 105425 Sorted by model distance: nonbonded pdb=" OD1 ASP A 213 " pdb=" OE1 GLN A 214 " model vdw 1.731 3.040 nonbonded pdb=" O2B ATP C 501 " pdb="MG MG C 502 " model vdw 1.997 2.170 nonbonded pdb=" O2B ATP A 501 " pdb="MG MG A 502 " model vdw 2.008 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 2.009 2.170 nonbonded pdb=" OG1 THR C 161 " pdb="MG MG C 502 " model vdw 2.026 2.170 ... (remaining 105420 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 87 through 221 or resid 231 through 342)) selection = (chain 'B' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'C' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'D' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'E' and (resid 87 through 132 or resid 145 through 221 or resid 231 throu \ gh 243 or resid 252 through 342)) selection = (chain 'F' and (resid 87 through 132 or resid 145 through 243 or resid 252 throu \ gh 342)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.520 Find NCS groups from input model: 0.300 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.004 0.079 13408 Z= 0.319 Angle : 0.944 22.839 18162 Z= 0.687 Chirality : 0.049 0.480 2061 Planarity : 0.006 0.114 2340 Dihedral : 11.873 82.824 5250 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 42.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.34 % Favored : 88.54 % Rotamer: Outliers : 0.93 % Allowed : 5.65 % Favored : 93.42 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.18), residues: 1632 helix: -1.98 (0.16), residues: 715 sheet: -2.31 (0.43), residues: 127 loop : -3.12 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 275 TYR 0.018 0.001 TYR D 129 PHE 0.018 0.002 PHE C 307 TRP 0.046 0.004 TRP D 241 HIS 0.013 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00431 (13408) covalent geometry : angle 0.94363 (18162) hydrogen bonds : bond 0.20607 ( 475) hydrogen bonds : angle 7.16242 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 418 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 128 ILE cc_start: 0.8359 (pp) cc_final: 0.8134 (mt) REVERT: F 269 ASP cc_start: 0.7012 (t0) cc_final: 0.6780 (t0) REVERT: A 174 SER cc_start: 0.8378 (m) cc_final: 0.6177 (m) REVERT: B 55 GLU cc_start: 0.5997 (tm-30) cc_final: 0.5749 (tm-30) REVERT: B 263 ASN cc_start: 0.7664 (m110) cc_final: 0.7455 (m110) REVERT: B 342 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: C 105 ASP cc_start: 0.7548 (t0) cc_final: 0.7105 (t0) REVERT: C 148 SER cc_start: 0.8727 (t) cc_final: 0.8484 (m) REVERT: C 298 LEU cc_start: 0.8676 (mt) cc_final: 0.8423 (mt) outliers start: 13 outliers final: 7 residues processed: 429 average time/residue: 0.1461 time to fit residues: 84.5378 Evaluate side-chains 213 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN A 94 ASN B 94 ASN B 192 ASN B 254 ASN B 279 GLN C 94 ASN C 169 HIS C 192 ASN C 214 GLN C 248 ASN D 214 GLN D 248 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 248 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103941 restraints weight = 26619.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104197 restraints weight = 18263.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105419 restraints weight = 15176.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105805 restraints weight = 13063.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105960 restraints weight = 11818.999| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13408 Z= 0.205 Angle : 0.834 12.351 18162 Z= 0.418 Chirality : 0.050 0.272 2061 Planarity : 0.007 0.114 2340 Dihedral : 11.293 88.959 2016 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.09 % Favored : 88.85 % Rotamer: Outliers : 3.79 % Allowed : 13.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.19), residues: 1632 helix: -1.18 (0.18), residues: 721 sheet: -1.89 (0.42), residues: 131 loop : -2.85 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 48 TYR 0.019 0.002 TYR F 137 PHE 0.016 0.002 PHE A 199 TRP 0.029 0.002 TRP C 241 HIS 0.006 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00487 (13408) covalent geometry : angle 0.83398 (18162) hydrogen bonds : bond 0.04572 ( 475) hydrogen bonds : angle 5.27946 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 190 ASP cc_start: 0.7240 (p0) cc_final: 0.7004 (t70) REVERT: F 192 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7896 (m-40) REVERT: F 263 ASN cc_start: 0.7929 (p0) cc_final: 0.7640 (p0) REVERT: F 268 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7015 (tp) REVERT: F 272 ILE cc_start: 0.8809 (mt) cc_final: 0.8595 (mp) REVERT: B 187 TRP cc_start: 0.8440 (m-10) cc_final: 0.8177 (m-10) REVERT: B 263 ASN cc_start: 0.7671 (m110) cc_final: 0.7411 (m110) REVERT: B 342 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: C 105 ASP cc_start: 0.7644 (t0) cc_final: 0.7182 (t0) REVERT: C 111 ASN cc_start: 0.7688 (t0) cc_final: 0.7419 (t0) REVERT: C 148 SER cc_start: 0.8693 (t) cc_final: 0.8467 (m) REVERT: C 303 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6529 (pmt100) REVERT: E 133 MET cc_start: 0.8734 (ppp) cc_final: 0.8521 (ppp) REVERT: E 232 MET cc_start: 0.8244 (ptm) cc_final: 0.7904 (ptm) outliers start: 53 outliers final: 34 residues processed: 251 average time/residue: 0.1116 time to fit residues: 40.6992 Evaluate side-chains 218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN A 94 ASN A 206 GLN B 343 HIS D 214 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103645 restraints weight = 26756.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104040 restraints weight = 18053.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104898 restraints weight = 14325.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105145 restraints weight = 13285.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105340 restraints weight = 12170.700| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13408 Z= 0.166 Angle : 0.748 9.946 18162 Z= 0.379 Chirality : 0.047 0.228 2061 Planarity : 0.006 0.110 2340 Dihedral : 10.843 89.944 2013 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.23 % Favored : 89.71 % Rotamer: Outliers : 5.15 % Allowed : 15.23 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.20), residues: 1632 helix: -0.75 (0.19), residues: 712 sheet: -1.36 (0.43), residues: 126 loop : -2.75 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.015 0.001 TYR E 92 PHE 0.013 0.002 PHE A 280 TRP 0.022 0.002 TRP C 241 HIS 0.004 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00389 (13408) covalent geometry : angle 0.74765 (18162) hydrogen bonds : bond 0.04014 ( 475) hydrogen bonds : angle 5.02216 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7232 (t80) REVERT: F 93 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: F 137 TYR cc_start: 0.5366 (t80) cc_final: 0.5110 (t80) REVERT: F 213 ASP cc_start: 0.6755 (t0) cc_final: 0.6500 (t0) REVERT: F 268 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7001 (tp) REVERT: A 62 ARG cc_start: 0.8217 (tpt170) cc_final: 0.7833 (tpt170) REVERT: B 187 TRP cc_start: 0.8441 (m-10) cc_final: 0.8203 (m-10) REVERT: B 263 ASN cc_start: 0.7571 (m110) cc_final: 0.7356 (m110) REVERT: B 342 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6719 (tt0) REVERT: C 105 ASP cc_start: 0.7437 (t0) cc_final: 0.7014 (t0) REVERT: C 111 ASN cc_start: 0.7757 (t0) cc_final: 0.7401 (t0) REVERT: C 148 SER cc_start: 0.8665 (t) cc_final: 0.8432 (m) REVERT: C 303 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6579 (pmt100) REVERT: E 232 MET cc_start: 0.8108 (ptm) cc_final: 0.7795 (ptm) outliers start: 72 outliers final: 41 residues processed: 252 average time/residue: 0.1097 time to fit residues: 40.2017 Evaluate side-chains 224 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN B 214 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 214 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101101 restraints weight = 26763.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101189 restraints weight = 18273.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102220 restraints weight = 15433.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102556 restraints weight = 13847.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102643 restraints weight = 12428.788| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13408 Z= 0.189 Angle : 0.766 10.444 18162 Z= 0.383 Chirality : 0.047 0.230 2061 Planarity : 0.006 0.110 2340 Dihedral : 10.716 88.336 2013 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.21 % Favored : 88.73 % Rotamer: Outliers : 5.79 % Allowed : 16.44 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.20), residues: 1632 helix: -0.58 (0.19), residues: 721 sheet: -0.95 (0.46), residues: 121 loop : -2.60 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 59 TYR 0.014 0.002 TYR D 153 PHE 0.013 0.002 PHE A 110 TRP 0.018 0.002 TRP C 241 HIS 0.004 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00450 (13408) covalent geometry : angle 0.76622 (18162) hydrogen bonds : bond 0.03802 ( 475) hydrogen bonds : angle 4.89934 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 181 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7879 (t80) REVERT: F 137 TYR cc_start: 0.5863 (t80) cc_final: 0.4989 (t80) REVERT: F 268 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7082 (tp) REVERT: A 62 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7755 (tpt170) REVERT: A 184 THR cc_start: 0.9201 (p) cc_final: 0.8914 (p) REVERT: A 333 MET cc_start: 0.8638 (tpp) cc_final: 0.8432 (tpp) REVERT: B 187 TRP cc_start: 0.8510 (m-10) cc_final: 0.8296 (m-10) REVERT: B 232 MET cc_start: 0.8229 (ttm) cc_final: 0.7975 (mtp) REVERT: B 263 ASN cc_start: 0.7575 (m110) cc_final: 0.7359 (m110) REVERT: B 319 MET cc_start: 0.8643 (ttm) cc_final: 0.8382 (ttm) REVERT: C 59 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7844 (tpp80) REVERT: C 105 ASP cc_start: 0.7466 (t0) cc_final: 0.7068 (t0) REVERT: C 111 ASN cc_start: 0.7937 (t0) cc_final: 0.7566 (t0) REVERT: C 148 SER cc_start: 0.8749 (t) cc_final: 0.8507 (m) REVERT: C 303 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6809 (pmt100) REVERT: E 133 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.7442 (ppp) REVERT: E 232 MET cc_start: 0.8030 (ptm) cc_final: 0.7717 (ptm) outliers start: 81 outliers final: 54 residues processed: 240 average time/residue: 0.1052 time to fit residues: 37.1355 Evaluate side-chains 227 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 325 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 214 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102959 restraints weight = 27108.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103116 restraints weight = 19218.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104540 restraints weight = 15521.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104915 restraints weight = 13371.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104995 restraints weight = 12056.693| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13408 Z= 0.134 Angle : 0.715 8.706 18162 Z= 0.359 Chirality : 0.045 0.213 2061 Planarity : 0.006 0.107 2340 Dihedral : 10.421 86.172 2010 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.80 % Favored : 90.13 % Rotamer: Outliers : 5.22 % Allowed : 18.37 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.21), residues: 1632 helix: -0.26 (0.20), residues: 708 sheet: -0.65 (0.48), residues: 121 loop : -2.51 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 59 TYR 0.014 0.001 TYR D 153 PHE 0.011 0.001 PHE A 280 TRP 0.015 0.001 TRP C 241 HIS 0.014 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00303 (13408) covalent geometry : angle 0.71501 (18162) hydrogen bonds : bond 0.03448 ( 475) hydrogen bonds : angle 4.75957 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 193 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7872 (t80) REVERT: F 93 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: F 137 TYR cc_start: 0.6231 (t80) cc_final: 0.5413 (t80) REVERT: F 268 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7008 (tp) REVERT: F 333 MET cc_start: 0.4743 (tpt) cc_final: 0.3671 (tpt) REVERT: A 184 THR cc_start: 0.9192 (p) cc_final: 0.8914 (p) REVERT: B 95 GLN cc_start: 0.7721 (pt0) cc_final: 0.7479 (pt0) REVERT: B 263 ASN cc_start: 0.7559 (m110) cc_final: 0.7342 (m110) REVERT: C 105 ASP cc_start: 0.7443 (t0) cc_final: 0.7077 (t0) REVERT: C 111 ASN cc_start: 0.7918 (t0) cc_final: 0.7541 (t0) REVERT: C 148 SER cc_start: 0.8743 (t) cc_final: 0.8496 (m) REVERT: C 303 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6569 (pmt100) REVERT: E 133 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7433 (ppp) REVERT: E 232 MET cc_start: 0.7925 (ptm) cc_final: 0.7624 (ptm) outliers start: 73 outliers final: 48 residues processed: 247 average time/residue: 0.1017 time to fit residues: 37.3436 Evaluate side-chains 230 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 141 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 94 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN B 192 ASN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102689 restraints weight = 26964.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102773 restraints weight = 19139.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103532 restraints weight = 15195.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104394 restraints weight = 13763.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104477 restraints weight = 12446.849| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13408 Z= 0.139 Angle : 0.720 10.140 18162 Z= 0.359 Chirality : 0.046 0.185 2061 Planarity : 0.006 0.105 2340 Dihedral : 10.399 89.960 2008 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.43 % Allowed : 18.37 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.84 (0.21), residues: 1632 helix: -0.14 (0.20), residues: 710 sheet: -0.53 (0.49), residues: 121 loop : -2.41 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.018 0.001 TYR D 153 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP D 241 HIS 0.011 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00321 (13408) covalent geometry : angle 0.71975 (18162) hydrogen bonds : bond 0.03439 ( 475) hydrogen bonds : angle 4.72927 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 187 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8319 (tp) REVERT: F 90 ASN cc_start: 0.8363 (t0) cc_final: 0.8039 (t0) REVERT: F 92 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7845 (t80) REVERT: F 93 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: F 268 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7025 (tp) REVERT: A 55 GLU cc_start: 0.5833 (tm-30) cc_final: 0.4782 (tm-30) REVERT: A 184 THR cc_start: 0.9206 (p) cc_final: 0.8930 (p) REVERT: A 259 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7560 (tt) REVERT: A 279 GLN cc_start: 0.8172 (pt0) cc_final: 0.7852 (mp-120) REVERT: B 93 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: B 263 ASN cc_start: 0.7563 (m110) cc_final: 0.7349 (m110) REVERT: C 105 ASP cc_start: 0.7482 (t0) cc_final: 0.7104 (t0) REVERT: C 111 ASN cc_start: 0.7959 (t0) cc_final: 0.7561 (t0) REVERT: C 148 SER cc_start: 0.8762 (t) cc_final: 0.8530 (m) REVERT: C 176 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 303 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6740 (pmt100) REVERT: E 133 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7463 (ppp) REVERT: E 232 MET cc_start: 0.7898 (ptm) cc_final: 0.7573 (ptm) outliers start: 76 outliers final: 50 residues processed: 239 average time/residue: 0.1031 time to fit residues: 36.5690 Evaluate side-chains 226 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 94 ASN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101359 restraints weight = 26813.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101706 restraints weight = 18511.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102645 restraints weight = 15109.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102910 restraints weight = 14402.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103124 restraints weight = 13030.664| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13408 Z= 0.152 Angle : 0.727 9.146 18162 Z= 0.363 Chirality : 0.046 0.226 2061 Planarity : 0.006 0.105 2340 Dihedral : 10.438 88.035 2004 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.17 % Favored : 89.77 % Rotamer: Outliers : 5.08 % Allowed : 18.58 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.72 (0.21), residues: 1632 helix: -0.06 (0.20), residues: 715 sheet: -0.46 (0.49), residues: 121 loop : -2.33 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 62 TYR 0.024 0.001 TYR D 43 PHE 0.012 0.002 PHE B 199 TRP 0.014 0.002 TRP C 241 HIS 0.009 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00357 (13408) covalent geometry : angle 0.72737 (18162) hydrogen bonds : bond 0.03418 ( 475) hydrogen bonds : angle 4.69067 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8307 (tp) REVERT: F 91 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: F 92 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7854 (t80) REVERT: F 268 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.6998 (tp) REVERT: A 55 GLU cc_start: 0.5953 (tm-30) cc_final: 0.5131 (tm-30) REVERT: A 62 ARG cc_start: 0.7988 (tpt170) cc_final: 0.7635 (tpt170) REVERT: A 184 THR cc_start: 0.9244 (p) cc_final: 0.8954 (p) REVERT: A 259 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7564 (tt) REVERT: A 279 GLN cc_start: 0.8179 (pt0) cc_final: 0.7867 (mp-120) REVERT: B 93 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: C 105 ASP cc_start: 0.7495 (t0) cc_final: 0.7159 (t0) REVERT: C 111 ASN cc_start: 0.8007 (t0) cc_final: 0.7609 (t0) REVERT: C 148 SER cc_start: 0.8790 (t) cc_final: 0.8557 (m) REVERT: C 176 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 303 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6872 (pmt100) REVERT: E 133 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7486 (ppp) REVERT: E 232 MET cc_start: 0.7876 (ptm) cc_final: 0.7396 (ptm) outliers start: 71 outliers final: 53 residues processed: 228 average time/residue: 0.0977 time to fit residues: 33.5124 Evaluate side-chains 228 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 325 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 254 ASN B 192 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.128485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103064 restraints weight = 26745.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103441 restraints weight = 18524.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104467 restraints weight = 15145.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104770 restraints weight = 13904.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104979 restraints weight = 12373.435| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13408 Z= 0.138 Angle : 0.734 10.036 18162 Z= 0.368 Chirality : 0.046 0.259 2061 Planarity : 0.006 0.104 2340 Dihedral : 10.179 86.974 2001 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.08 % Allowed : 18.87 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.62 (0.21), residues: 1632 helix: 0.01 (0.20), residues: 709 sheet: -0.45 (0.49), residues: 120 loop : -2.24 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.037 0.001 TYR D 153 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP C 241 HIS 0.008 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00317 (13408) covalent geometry : angle 0.73385 (18162) hydrogen bonds : bond 0.03341 ( 475) hydrogen bonds : angle 4.68610 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 171 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7917 (t80) REVERT: F 268 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.6955 (tp) REVERT: F 336 MET cc_start: 0.6012 (ppp) cc_final: 0.5435 (ppp) REVERT: A 55 GLU cc_start: 0.5903 (tm-30) cc_final: 0.5266 (tm-30) REVERT: A 62 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7540 (tpt170) REVERT: A 184 THR cc_start: 0.9225 (p) cc_final: 0.8928 (p) REVERT: A 259 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7536 (tt) REVERT: A 268 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 269 ASP cc_start: 0.5575 (p0) cc_final: 0.5120 (p0) REVERT: A 279 GLN cc_start: 0.8121 (pt0) cc_final: 0.7855 (mp-120) REVERT: B 59 ARG cc_start: 0.6069 (tmm160) cc_final: 0.5862 (tmm160) REVERT: B 93 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: C 105 ASP cc_start: 0.7541 (t0) cc_final: 0.7201 (t0) REVERT: C 111 ASN cc_start: 0.8013 (t0) cc_final: 0.7625 (t0) REVERT: C 148 SER cc_start: 0.8784 (t) cc_final: 0.8551 (m) REVERT: C 176 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 303 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6732 (pmt100) REVERT: E 133 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7455 (ppp) outliers start: 71 outliers final: 53 residues processed: 219 average time/residue: 0.0976 time to fit residues: 32.2969 Evaluate side-chains 228 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 158 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 95 GLN ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 254 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS D 214 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102322 restraints weight = 26937.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102503 restraints weight = 18432.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103002 restraints weight = 15402.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103455 restraints weight = 15427.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103825 restraints weight = 13197.637| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13408 Z= 0.147 Angle : 0.735 10.576 18162 Z= 0.367 Chirality : 0.046 0.249 2061 Planarity : 0.006 0.104 2340 Dihedral : 10.093 87.995 1999 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.11 % Favored : 89.83 % Rotamer: Outliers : 4.79 % Allowed : 19.30 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.52 (0.21), residues: 1632 helix: 0.08 (0.20), residues: 706 sheet: -0.36 (0.49), residues: 120 loop : -2.17 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.033 0.001 TYR D 153 PHE 0.012 0.001 PHE A 280 TRP 0.013 0.001 TRP C 241 HIS 0.008 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00346 (13408) covalent geometry : angle 0.73476 (18162) hydrogen bonds : bond 0.03354 ( 475) hydrogen bonds : angle 4.63007 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7955 (t80) REVERT: F 269 ASP cc_start: 0.6885 (t0) cc_final: 0.6349 (t0) REVERT: F 272 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8557 (mp) REVERT: F 336 MET cc_start: 0.5886 (ppp) cc_final: 0.5458 (ppp) REVERT: A 55 GLU cc_start: 0.6040 (tm-30) cc_final: 0.5457 (tm-30) REVERT: A 62 ARG cc_start: 0.7964 (tpt170) cc_final: 0.7604 (tpt170) REVERT: A 184 THR cc_start: 0.9223 (p) cc_final: 0.8936 (p) REVERT: A 279 GLN cc_start: 0.8145 (pt0) cc_final: 0.7871 (mp-120) REVERT: B 93 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: C 105 ASP cc_start: 0.7608 (t0) cc_final: 0.7263 (t0) REVERT: C 111 ASN cc_start: 0.8066 (t0) cc_final: 0.7666 (t0) REVERT: C 148 SER cc_start: 0.8788 (t) cc_final: 0.8558 (m) REVERT: C 176 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8556 (mt) REVERT: C 303 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6897 (pmt100) REVERT: E 133 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7464 (ppp) outliers start: 67 outliers final: 49 residues processed: 213 average time/residue: 0.0951 time to fit residues: 31.0028 Evaluate side-chains 217 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 110 PHE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 254 ASN Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 141 optimal weight: 0.0470 chunk 138 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 30 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 192 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN C 94 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.139553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110254 restraints weight = 27836.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113340 restraints weight = 15915.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115393 restraints weight = 11238.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116721 restraints weight = 9050.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.117393 restraints weight = 7913.244| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13408 Z= 0.131 Angle : 0.731 11.205 18162 Z= 0.364 Chirality : 0.045 0.230 2061 Planarity : 0.006 0.102 2340 Dihedral : 9.904 89.263 1999 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.86 % Allowed : 20.37 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.39 (0.21), residues: 1632 helix: 0.19 (0.20), residues: 703 sheet: -0.08 (0.49), residues: 115 loop : -2.13 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 62 TYR 0.032 0.001 TYR D 153 PHE 0.010 0.001 PHE C 175 TRP 0.012 0.001 TRP C 241 HIS 0.003 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00294 (13408) covalent geometry : angle 0.73132 (18162) hydrogen bonds : bond 0.03221 ( 475) hydrogen bonds : angle 4.60382 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7911 (t80) REVERT: F 192 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8013 (m-40) REVERT: F 336 MET cc_start: 0.6191 (ppp) cc_final: 0.5868 (ppp) REVERT: A 55 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5697 (tm-30) REVERT: A 62 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7704 (tpt170) REVERT: A 184 THR cc_start: 0.9232 (p) cc_final: 0.8948 (p) REVERT: A 279 GLN cc_start: 0.8351 (pt0) cc_final: 0.7889 (mp-120) REVERT: B 59 ARG cc_start: 0.5989 (tmm160) cc_final: 0.5585 (tmm160) REVERT: B 93 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: C 94 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8472 (t0) REVERT: C 105 ASP cc_start: 0.7854 (t0) cc_final: 0.7495 (t0) REVERT: C 111 ASN cc_start: 0.8331 (t0) cc_final: 0.7945 (t0) REVERT: C 303 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6727 (pmt100) REVERT: E 133 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7452 (ppp) outliers start: 54 outliers final: 41 residues processed: 209 average time/residue: 0.1082 time to fit residues: 34.0752 Evaluate side-chains 214 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 241 TRP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 343 HIS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 179 HIS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 116 optimal weight: 0.9980 chunk 134 optimal weight: 0.0020 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN F 254 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.139517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110223 restraints weight = 27649.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113361 restraints weight = 15632.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.115367 restraints weight = 11015.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116684 restraints weight = 8903.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117173 restraints weight = 7786.075| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 13408 Z= 0.235 Angle : 1.153 59.132 18162 Z= 0.698 Chirality : 0.065 1.983 2061 Planarity : 0.007 0.147 2340 Dihedral : 9.930 89.237 1999 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.00 % Allowed : 20.37 % Favored : 75.63 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % 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: -1.41 (0.21), residues: 1632 helix: 0.15 (0.20), residues: 702 sheet: -0.06 (0.49), residues: 115 loop : -2.12 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 62 TYR 0.029 0.001 TYR D 153 PHE 0.010 0.001 PHE C 175 TRP 0.011 0.001 TRP C 241 HIS 0.003 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00493 (13408) covalent geometry : angle 1.15337 (18162) hydrogen bonds : bond 0.03293 ( 475) hydrogen bonds : angle 4.60722 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.10 seconds wall clock time: 36 minutes 18.62 seconds (2178.62 seconds total)