Starting phenix.real_space_refine on Thu Jul 31 08:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pe0_20320/07_2025/6pe0_20320_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pe0_20320/07_2025/6pe0_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_20320/07_2025/6pe0_20320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pe0_20320/07_2025/6pe0_20320.map" model { file = "/net/cci-nas-00/data/ceres_data/6pe0_20320/07_2025/6pe0_20320_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pe0_20320/07_2025/6pe0_20320_neut_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.83, per 1000 atoms: 0.67 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: 3.43 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.56 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: 3.88 Time building geometry restraints manager: 3.81 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: 1.660 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.690 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (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 TRP 0.046 0.004 TRP D 241 HIS 0.013 0.001 HIS A 179 PHE 0.018 0.002 PHE C 307 TYR 0.018 0.001 TYR D 129 ARG 0.009 0.001 ARG F 275 Details of bonding type rmsd hydrogen bonds : bond 0.20607 ( 475) hydrogen bonds : angle 7.16242 ( 1335) covalent geometry : bond 0.00431 (13408) covalent geometry : angle 0.94363 (18162) *********************** 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 : 1.643 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: F 128 ILE cc_start: 0.8359 (pp) cc_final: 0.8141 (mt) REVERT: F 269 ASP cc_start: 0.7012 (t0) cc_final: 0.6782 (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: 0.8372 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: C 105 ASP cc_start: 0.7548 (t0) cc_final: 0.7104 (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: 0.8419 (mt) outliers start: 13 outliers final: 7 residues processed: 429 average time/residue: 0.3186 time to fit residues: 183.3110 Evaluate side-chains 215 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3831 r_free = 0.3831 target = 0.130542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105479 restraints weight = 26520.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106114 restraints weight = 18932.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107230 restraints weight = 15033.257| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13408 Z= 0.174 Angle : 0.816 12.347 18162 Z= 0.410 Chirality : 0.049 0.237 2061 Planarity : 0.008 0.187 2340 Dihedral : 11.226 89.022 2016 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.03 % Favored : 88.91 % Rotamer: Outliers : 3.79 % Allowed : 14.08 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.19), residues: 1632 helix: -1.09 (0.18), residues: 716 sheet: -1.84 (0.42), residues: 131 loop : -2.86 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 241 HIS 0.006 0.001 HIS E 139 PHE 0.017 0.002 PHE A 199 TYR 0.021 0.002 TYR F 137 ARG 0.022 0.001 ARG F 292 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 475) hydrogen bonds : angle 5.23746 ( 1335) covalent geometry : bond 0.00401 (13408) covalent geometry : angle 0.81604 (18162) *********************** 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 281 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 1.585 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 92 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7023 (t80) REVERT: F 93 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: F 263 ASN cc_start: 0.7889 (p0) cc_final: 0.7645 (p0) REVERT: F 268 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7034 (tp) REVERT: F 272 ILE cc_start: 0.8804 (mt) cc_final: 0.8594 (mp) REVERT: B 187 TRP cc_start: 0.8420 (m-10) cc_final: 0.8163 (m-10) REVERT: B 263 ASN cc_start: 0.7731 (m110) cc_final: 0.7475 (m110) REVERT: B 342 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: C 105 ASP cc_start: 0.7579 (t0) cc_final: 0.7108 (t0) REVERT: C 111 ASN cc_start: 0.7675 (t0) cc_final: 0.7397 (t0) REVERT: C 131 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 148 SER cc_start: 0.8676 (t) cc_final: 0.8416 (m) REVERT: C 303 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6565 (pmt100) REVERT: E 133 MET cc_start: 0.8709 (ppp) cc_final: 0.8497 (ppp) REVERT: E 232 MET cc_start: 0.8239 (ptm) cc_final: 0.7860 (ptm) outliers start: 53 outliers final: 34 residues processed: 259 average time/residue: 0.2597 time to fit residues: 97.4561 Evaluate side-chains 229 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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 129 TYR Chi-restraints excluded: chain F residue 135 HIS 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 209 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 98 LEU 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 131 LEU 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 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 118 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 24 optimal weight: 40.0000 chunk 91 optimal weight: 0.5980 chunk 33 optimal weight: 0.0170 chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** A 206 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105697 restraints weight = 26923.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106041 restraints weight = 18452.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.107184 restraints weight = 14682.854| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13408 Z= 0.148 Angle : 0.738 9.997 18162 Z= 0.371 Chirality : 0.046 0.235 2061 Planarity : 0.006 0.113 2340 Dihedral : 10.604 85.901 2013 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer: Outliers : 4.65 % Allowed : 15.80 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1632 helix: -0.76 (0.19), residues: 725 sheet: -1.28 (0.43), residues: 126 loop : -2.68 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 241 HIS 0.003 0.001 HIS D 343 PHE 0.010 0.002 PHE E 237 TYR 0.021 0.001 TYR D 153 ARG 0.005 0.001 ARG F 292 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 475) hydrogen bonds : angle 4.97825 ( 1335) covalent geometry : bond 0.00333 (13408) covalent geometry : angle 0.73805 (18162) *********************** 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 271 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 1.550 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: 0.8199 (OUTLIER) cc_final: 0.7723 (t80) REVERT: F 93 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: F 213 ASP cc_start: 0.6662 (t0) cc_final: 0.6299 (t0) REVERT: F 268 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 62 ARG cc_start: 0.8276 (tpt170) cc_final: 0.7911 (tpt170) REVERT: A 89 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6892 (pp) REVERT: A 184 THR cc_start: 0.9183 (p) cc_final: 0.8930 (p) REVERT: B 187 TRP cc_start: 0.8417 (m-10) cc_final: 0.8209 (m-10) REVERT: B 232 MET cc_start: 0.8175 (ttm) cc_final: 0.7954 (ttm) REVERT: B 263 ASN cc_start: 0.7553 (m110) cc_final: 0.7336 (m110) REVERT: C 51 ILE cc_start: 0.8339 (tp) cc_final: 0.7760 (tt) REVERT: C 105 ASP cc_start: 0.7424 (t0) cc_final: 0.7016 (t0) REVERT: C 111 ASN cc_start: 0.7760 (t0) cc_final: 0.7378 (t0) REVERT: C 148 SER cc_start: 0.8670 (t) cc_final: 0.8463 (m) REVERT: C 303 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6457 (pmt100) REVERT: D 153 TYR cc_start: 0.8103 (p90) cc_final: 0.7880 (p90) REVERT: E 232 MET cc_start: 0.8207 (ptm) cc_final: 0.7868 (ptm) outliers start: 65 outliers final: 35 residues processed: 253 average time/residue: 0.2755 time to fit residues: 102.4047 Evaluate side-chains 220 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 89 LEU 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 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 343 HIS Chi-restraints excluded: chain B residue 344 ARG 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 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 106 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 282 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 114 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN B 343 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 214 GLN ** D 289 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 = 0.3777 r_free = 0.3777 target = 0.126301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101520 restraints weight = 26414.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101522 restraints weight = 18638.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102529 restraints weight = 16008.853| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13408 Z= 0.207 Angle : 0.779 15.224 18162 Z= 0.389 Chirality : 0.048 0.192 2061 Planarity : 0.007 0.136 2340 Dihedral : 10.550 87.529 2010 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.97 % Favored : 88.97 % Rotamer: Outliers : 5.36 % Allowed : 17.16 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1632 helix: -0.58 (0.19), residues: 728 sheet: -0.80 (0.48), residues: 121 loop : -2.50 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 241 HIS 0.004 0.001 HIS A 179 PHE 0.013 0.002 PHE B 199 TYR 0.020 0.002 TYR F 137 ARG 0.009 0.001 ARG F 292 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 475) hydrogen bonds : angle 4.92697 ( 1335) covalent geometry : bond 0.00498 (13408) covalent geometry : angle 0.77934 (18162) *********************** 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 259 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 1.496 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: 0.8260 (OUTLIER) cc_final: 0.7867 (t80) REVERT: F 268 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7171 (tt) REVERT: A 62 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7743 (tpt170) REVERT: A 184 THR cc_start: 0.9210 (p) cc_final: 0.8931 (p) REVERT: A 333 MET cc_start: 0.8616 (tpp) cc_final: 0.8413 (tpp) REVERT: B 187 TRP cc_start: 0.8501 (m-10) cc_final: 0.8295 (m-10) REVERT: B 232 MET cc_start: 0.8215 (ttm) cc_final: 0.7949 (mtp) REVERT: B 263 ASN cc_start: 0.7600 (m110) cc_final: 0.7359 (m110) REVERT: C 105 ASP cc_start: 0.7508 (t0) cc_final: 0.7122 (t0) REVERT: C 111 ASN cc_start: 0.7913 (t0) cc_final: 0.7520 (t0) REVERT: C 131 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8652 (tp) REVERT: C 148 SER cc_start: 0.8755 (t) cc_final: 0.8514 (m) REVERT: C 303 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6889 (pmt100) REVERT: E 133 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7431 (ppp) REVERT: E 232 MET cc_start: 0.8053 (ptm) cc_final: 0.7694 (ptm) outliers start: 75 outliers final: 44 residues processed: 240 average time/residue: 0.2456 time to fit residues: 85.9817 Evaluate side-chains 217 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 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 198 VAL 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 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 108 VAL Chi-restraints excluded: chain C residue 131 LEU 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 120 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 240 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 0.0970 chunk 121 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 ASN B 214 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3778 r_free = 0.3778 target = 0.126425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.101103 restraints weight = 26699.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101162 restraints weight = 18280.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101927 restraints weight = 16131.073| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4454 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 : 0.737 8.859 18162 Z= 0.369 Chirality : 0.046 0.199 2061 Planarity : 0.006 0.108 2340 Dihedral : 10.498 87.986 2008 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.42 % Favored : 89.46 % Rotamer: Outliers : 5.29 % Allowed : 18.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1632 helix: -0.40 (0.19), residues: 728 sheet: -0.65 (0.49), residues: 118 loop : -2.40 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 241 HIS 0.014 0.001 HIS C 227 PHE 0.012 0.002 PHE A 110 TYR 0.015 0.001 TYR D 153 ARG 0.004 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 475) hydrogen bonds : angle 4.83278 ( 1335) covalent geometry : bond 0.00394 (13408) covalent geometry : angle 0.73698 (18162) *********************** 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 252 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 178 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7583 (t80) REVERT: F 93 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: F 268 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7213 (tt) REVERT: A 55 GLU cc_start: 0.5938 (tm-30) cc_final: 0.5222 (tm-30) REVERT: A 92 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 184 THR cc_start: 0.9226 (p) cc_final: 0.8955 (p) REVERT: A 279 GLN cc_start: 0.8241 (pt0) cc_final: 0.7855 (mp-120) REVERT: B 106 ILE cc_start: 0.8253 (mm) cc_final: 0.8018 (mm) REVERT: B 232 MET cc_start: 0.8265 (ttm) cc_final: 0.8037 (mtm) REVERT: B 263 ASN cc_start: 0.7591 (m110) cc_final: 0.7379 (m110) REVERT: B 344 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8089 (tpp-160) REVERT: C 105 ASP cc_start: 0.7627 (t0) cc_final: 0.7224 (t0) REVERT: C 111 ASN cc_start: 0.8063 (t0) cc_final: 0.7692 (t0) REVERT: C 148 SER cc_start: 0.8806 (t) cc_final: 0.8574 (m) REVERT: C 303 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6962 (pmt100) REVERT: D 174 SER cc_start: 0.9030 (t) cc_final: 0.8730 (m) REVERT: E 133 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.7557 (ppp) REVERT: E 232 MET cc_start: 0.8095 (ptm) cc_final: 0.7745 (ptm) outliers start: 74 outliers final: 49 residues processed: 227 average time/residue: 0.2769 time to fit residues: 93.1481 Evaluate side-chains 225 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 98 LEU 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 304 ASP Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 198 VAL 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 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 179 HIS Chi-restraints excluded: chain C residue 180 ILE 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 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 240 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 ILE 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 80 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 132 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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** C 94 ASN ** 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 = 0.3776 r_free = 0.3776 target = 0.126371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101281 restraints weight = 26994.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100884 restraints weight = 19074.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101857 restraints weight = 16256.420| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4638 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= 0.158 Angle : 0.734 9.260 18162 Z= 0.366 Chirality : 0.046 0.215 2061 Planarity : 0.006 0.106 2340 Dihedral : 10.510 88.168 2008 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.36 % Favored : 89.58 % Rotamer: Outliers : 5.65 % Allowed : 18.08 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1632 helix: -0.22 (0.20), residues: 723 sheet: -0.53 (0.50), residues: 118 loop : -2.35 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 241 HIS 0.010 0.001 HIS C 227 PHE 0.012 0.001 PHE C 175 TYR 0.017 0.001 TYR D 153 ARG 0.004 0.000 ARG D 275 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 475) hydrogen bonds : angle 4.78977 ( 1335) covalent geometry : bond 0.00373 (13408) covalent geometry : angle 0.73429 (18162) *********************** 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 265 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8434 (tp) REVERT: F 90 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8029 (t0) REVERT: F 92 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7731 (t80) REVERT: F 268 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7215 (tt) REVERT: A 55 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5422 (tm-30) REVERT: A 62 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7778 (tpt170) REVERT: A 92 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6144 (t80) REVERT: A 184 THR cc_start: 0.9227 (p) cc_final: 0.8954 (p) REVERT: A 232 MET cc_start: 0.6904 (ptt) cc_final: 0.6701 (ptt) REVERT: A 259 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 279 GLN cc_start: 0.8275 (pt0) cc_final: 0.7899 (mp-120) REVERT: B 93 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: B 106 ILE cc_start: 0.8261 (mm) cc_final: 0.8037 (mm) REVERT: B 232 MET cc_start: 0.8278 (ttm) cc_final: 0.8035 (mtm) REVERT: B 263 ASN cc_start: 0.7580 (m110) cc_final: 0.7374 (m110) REVERT: B 344 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8074 (tpp-160) REVERT: C 105 ASP cc_start: 0.7643 (t0) cc_final: 0.7286 (t0) REVERT: C 111 ASN cc_start: 0.8074 (t0) cc_final: 0.7702 (t0) REVERT: C 148 SER cc_start: 0.8810 (t) cc_final: 0.8609 (m) REVERT: C 176 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8632 (mt) REVERT: C 303 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6949 (pmt100) REVERT: D 174 SER cc_start: 0.9009 (t) cc_final: 0.8676 (m) REVERT: D 214 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7686 (mm-40) REVERT: E 133 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.7568 (ppp) REVERT: E 232 MET cc_start: 0.8072 (ptm) cc_final: 0.7746 (ptm) outliers start: 79 outliers final: 48 residues processed: 241 average time/residue: 0.2676 time to fit residues: 94.5972 Evaluate side-chains 235 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 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 246 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 198 VAL 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 163 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 218 VAL 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 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 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 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 240 LEU 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 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 149 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 111 optimal weight: 0.0170 chunk 15 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 GLN F 254 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 139 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102539 restraints weight = 26646.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102128 restraints weight = 19301.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102658 restraints weight = 15766.721| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4791 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= 0.141 Angle : 0.745 10.614 18162 Z= 0.370 Chirality : 0.046 0.214 2061 Planarity : 0.006 0.104 2340 Dihedral : 10.245 89.186 2005 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 5.00 % Allowed : 18.73 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1632 helix: -0.07 (0.20), residues: 723 sheet: -0.46 (0.50), residues: 118 loop : -2.27 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 241 HIS 0.009 0.001 HIS C 227 PHE 0.011 0.001 PHE C 175 TYR 0.023 0.001 TYR D 43 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 475) hydrogen bonds : angle 4.73827 ( 1335) covalent geometry : bond 0.00328 (13408) covalent geometry : angle 0.74535 (18162) *********************** 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 260 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7658 (t80) REVERT: F 268 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.6987 (tp) REVERT: F 336 MET cc_start: 0.5788 (ppp) cc_final: 0.5361 (ppp) REVERT: A 55 GLU cc_start: 0.6096 (tm-30) cc_final: 0.5495 (tm-30) REVERT: A 184 THR cc_start: 0.9229 (p) cc_final: 0.8964 (p) REVERT: A 259 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7635 (tt) REVERT: A 279 GLN cc_start: 0.8167 (pt0) cc_final: 0.7895 (mp-120) REVERT: B 93 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: B 106 ILE cc_start: 0.8228 (mm) cc_final: 0.7998 (mm) REVERT: B 232 MET cc_start: 0.8176 (ttm) cc_final: 0.7916 (mtm) REVERT: B 263 ASN cc_start: 0.7522 (m110) cc_final: 0.7302 (m110) REVERT: B 344 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.8018 (tpp-160) REVERT: C 105 ASP cc_start: 0.7506 (t0) cc_final: 0.7151 (t0) REVERT: C 111 ASN cc_start: 0.7990 (t0) cc_final: 0.7622 (t0) REVERT: C 148 SER cc_start: 0.8768 (t) cc_final: 0.8542 (m) REVERT: C 176 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8627 (mt) REVERT: C 303 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6871 (pmt100) REVERT: D 174 SER cc_start: 0.8955 (t) cc_final: 0.8671 (m) REVERT: E 133 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7569 (ppp) REVERT: E 232 MET cc_start: 0.7927 (ptm) cc_final: 0.7408 (ptm) outliers start: 70 outliers final: 49 residues processed: 237 average time/residue: 0.3107 time to fit residues: 108.2182 Evaluate side-chains 232 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 139 HIS 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 268 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 198 VAL 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 216 ASP 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 B residue 344 ARG Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 176 ILE 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 307 PHE 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 129 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 LEU 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 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 340 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 42 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 254 ASN A 254 ASN B 342 GLN C 227 HIS D 56 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101305 restraints weight = 26891.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100993 restraints weight = 18819.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101659 restraints weight = 15761.650| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13408 Z= 0.153 Angle : 0.737 9.947 18162 Z= 0.366 Chirality : 0.046 0.182 2061 Planarity : 0.006 0.104 2340 Dihedral : 10.223 89.222 2003 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.36 % Favored : 89.58 % Rotamer: Outliers : 5.00 % Allowed : 19.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1632 helix: -0.04 (0.20), residues: 720 sheet: -0.41 (0.50), residues: 118 loop : -2.22 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 241 HIS 0.008 0.001 HIS C 227 PHE 0.012 0.001 PHE B 199 TYR 0.022 0.001 TYR D 153 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 475) hydrogen bonds : angle 4.69657 ( 1335) covalent geometry : bond 0.00360 (13408) covalent geometry : angle 0.73724 (18162) *********************** 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 249 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.8055 (t80) REVERT: F 268 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7039 (tp) REVERT: F 269 ASP cc_start: 0.6809 (t0) cc_final: 0.6548 (t0) REVERT: F 272 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 55 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5591 (tm-30) REVERT: A 62 ARG cc_start: 0.8033 (tpt170) cc_final: 0.7728 (tpt170) REVERT: A 92 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6401 (t80) REVERT: A 184 THR cc_start: 0.9243 (p) cc_final: 0.8966 (p) REVERT: A 279 GLN cc_start: 0.8229 (pt0) cc_final: 0.7918 (mp-120) REVERT: B 92 TYR cc_start: 0.6836 (t80) cc_final: 0.6621 (t80) REVERT: B 93 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: B 106 ILE cc_start: 0.8260 (mm) cc_final: 0.8040 (mm) REVERT: B 232 MET cc_start: 0.8219 (ttm) cc_final: 0.7960 (mtm) REVERT: B 263 ASN cc_start: 0.7542 (m110) cc_final: 0.7307 (m110) REVERT: C 105 ASP cc_start: 0.7560 (t0) cc_final: 0.7210 (t0) REVERT: C 111 ASN cc_start: 0.8023 (t0) cc_final: 0.7650 (t0) REVERT: C 148 SER cc_start: 0.8781 (t) cc_final: 0.8573 (m) REVERT: C 176 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8649 (mt) REVERT: C 303 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6908 (pmt100) REVERT: D 174 SER cc_start: 0.8970 (t) cc_final: 0.8703 (m) REVERT: E 54 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: E 133 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7559 (ppp) REVERT: E 232 MET cc_start: 0.7906 (ptm) cc_final: 0.7414 (ptm) outliers start: 70 outliers final: 49 residues processed: 227 average time/residue: 0.3362 time to fit residues: 113.1690 Evaluate side-chains 229 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 139 HIS 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 268 ILE 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 92 TYR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 198 VAL 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 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 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 D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 163 LEU 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 240 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 13 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102468 restraints weight = 26780.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102310 restraints weight = 18637.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102761 restraints weight = 15450.003| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5092 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= 0.135 Angle : 0.723 10.381 18162 Z= 0.358 Chirality : 0.045 0.216 2061 Planarity : 0.006 0.101 2340 Dihedral : 10.060 87.733 1999 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.65 % Allowed : 19.73 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1632 helix: 0.04 (0.20), residues: 718 sheet: -0.25 (0.50), residues: 118 loop : -2.14 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.005 0.001 HIS F 169 PHE 0.011 0.001 PHE C 175 TYR 0.025 0.001 TYR D 43 ARG 0.004 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 475) hydrogen bonds : angle 4.67664 ( 1335) covalent geometry : bond 0.00313 (13408) covalent geometry : angle 0.72330 (18162) *********************** 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 238 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7775 (t80) REVERT: F 268 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.6906 (tp) REVERT: F 269 ASP cc_start: 0.6840 (t0) cc_final: 0.6355 (t0) REVERT: F 272 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8468 (mp) REVERT: F 333 MET cc_start: 0.6910 (mmp) cc_final: 0.6632 (mmp) REVERT: A 55 GLU cc_start: 0.6103 (tm-30) cc_final: 0.5515 (tm-30) REVERT: A 62 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7631 (tpt170) REVERT: A 92 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6382 (t80) REVERT: A 184 THR cc_start: 0.9223 (p) cc_final: 0.8943 (p) REVERT: A 279 GLN cc_start: 0.8148 (pt0) cc_final: 0.7819 (mp10) REVERT: B 93 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: B 106 ILE cc_start: 0.8227 (mm) cc_final: 0.8018 (mm) REVERT: B 232 MET cc_start: 0.8226 (ttm) cc_final: 0.7933 (mtm) REVERT: B 263 ASN cc_start: 0.7628 (m110) cc_final: 0.7408 (m110) REVERT: C 105 ASP cc_start: 0.7631 (t0) cc_final: 0.7282 (t0) REVERT: C 111 ASN cc_start: 0.7999 (t0) cc_final: 0.7615 (t0) REVERT: C 303 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6824 (pmt100) REVERT: E 54 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: E 133 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7530 (ppp) outliers start: 65 outliers final: 47 residues processed: 217 average time/residue: 0.2743 time to fit residues: 88.6149 Evaluate side-chains 225 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 139 HIS 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 272 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain A residue 92 TYR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 198 VAL 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 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 343 HIS 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 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 D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 163 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.101645 restraints weight = 26649.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102207 restraints weight = 18263.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103047 restraints weight = 14919.174| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13408 Z= 0.142 Angle : 0.736 11.084 18162 Z= 0.365 Chirality : 0.046 0.245 2061 Planarity : 0.006 0.101 2340 Dihedral : 10.005 89.674 1999 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.54 % Favored : 89.40 % Rotamer: Outliers : 4.15 % Allowed : 20.80 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1632 helix: 0.09 (0.20), residues: 718 sheet: -0.19 (0.50), residues: 121 loop : -2.09 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 241 HIS 0.003 0.001 HIS D 343 PHE 0.015 0.001 PHE A 280 TYR 0.021 0.001 TYR D 153 ARG 0.005 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 475) hydrogen bonds : angle 4.63990 ( 1335) covalent geometry : bond 0.00330 (13408) covalent geometry : angle 0.73567 (18162) ********************** 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 228 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7767 (t80) REVERT: F 269 ASP cc_start: 0.6798 (t0) cc_final: 0.6249 (t0) REVERT: F 272 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8525 (mp) REVERT: F 336 MET cc_start: 0.6487 (ppp) cc_final: 0.6125 (ppp) REVERT: A 55 GLU cc_start: 0.5993 (tm-30) cc_final: 0.5419 (tm-30) REVERT: A 62 ARG cc_start: 0.7927 (tpt170) cc_final: 0.7606 (tpt170) REVERT: A 92 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6346 (t80) REVERT: A 184 THR cc_start: 0.9221 (p) cc_final: 0.8944 (p) REVERT: A 279 GLN cc_start: 0.8099 (pt0) cc_final: 0.7737 (mp10) REVERT: B 59 ARG cc_start: 0.6205 (tmm160) cc_final: 0.5782 (tmm160) REVERT: B 93 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: B 106 ILE cc_start: 0.8206 (mm) cc_final: 0.7998 (mm) REVERT: B 232 MET cc_start: 0.8233 (ttm) cc_final: 0.7946 (mtm) REVERT: B 263 ASN cc_start: 0.7641 (m110) cc_final: 0.7421 (m110) REVERT: C 105 ASP cc_start: 0.7719 (t0) cc_final: 0.7345 (t0) REVERT: C 111 ASN cc_start: 0.8074 (t0) cc_final: 0.7723 (t0) REVERT: C 303 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6824 (pmt100) REVERT: E 54 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: E 133 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7512 (ppp) outliers start: 58 outliers final: 47 residues processed: 211 average time/residue: 0.2418 time to fit residues: 76.8025 Evaluate side-chains 223 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 129 TYR Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 139 HIS Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 181 SER 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 92 TYR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 198 VAL 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 227 HIS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 343 HIS 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 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 D residue 108 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 163 LEU 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 244 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 54 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 78 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 116 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108482 restraints weight = 27859.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111565 restraints weight = 15805.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113589 restraints weight = 11219.591| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13408 Z= 0.129 Angle : 0.731 10.695 18162 Z= 0.363 Chirality : 0.045 0.234 2061 Planarity : 0.006 0.101 2340 Dihedral : 9.924 89.696 1999 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.86 % Allowed : 21.09 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1632 helix: 0.16 (0.20), residues: 717 sheet: -0.15 (0.50), residues: 118 loop : -2.03 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 241 HIS 0.003 0.001 HIS D 343 PHE 0.012 0.001 PHE C 175 TYR 0.029 0.001 TYR D 43 ARG 0.005 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 475) hydrogen bonds : angle 4.61590 ( 1335) covalent geometry : bond 0.00286 (13408) covalent geometry : angle 0.73059 (18162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.31 seconds wall clock time: 88 minutes 9.76 seconds (5289.76 seconds total)