Starting phenix.real_space_refine on Fri Jun 13 06:16:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.map" model { file = "/net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osf_17151/06_2025/8osf_17151.cif" } resolution = 4.0 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= 0.001 sd= 0.015 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 17 5.49 5 Mg 5 5.21 5 S 51 5.16 5 C 9124 2.51 5 N 2521 2.21 5 O 2811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14529 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2499 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain breaks: 2 Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1787 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 2 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} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.22, per 1000 atoms: 0.63 Number of scatterers: 14529 At special positions: 0 Unit cell: (130.284, 138.6, 77.616, 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 51 16.00 P 17 15.00 Mg 5 11.99 O 2811 8.00 N 2521 7.00 C 9124 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: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 49.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.591A pdb=" N ALA A 20 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 21 " --> pdb=" O PHE A 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 17 through 21' Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.377A pdb=" N LEU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.507A pdb=" N ARG A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.722A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.613A pdb=" N VAL A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N CYS A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 121' Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.598A pdb=" N GLY A 181 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.550A pdb=" N LEU A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.578A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 247 through 264 removed outlier: 4.358A pdb=" N GLN A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.545A pdb=" N ARG A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 308 removed outlier: 3.983A pdb=" N ILE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.930A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.613A pdb=" N LYS A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 removed outlier: 3.575A pdb=" N ALA B 20 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 21 " --> pdb=" O PHE B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 17 through 21' Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.596A pdb=" N ALA B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.930A pdb=" N ILE B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 32 through 37' Processing helix chain 'B' and resid 52 through 57 removed outlier: 4.077A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.702A pdb=" N ALA B 61 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 4.072A pdb=" N VAL B 120 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.986A pdb=" N LYS B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.051A pdb=" N ASP B 168 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 222 through 239 removed outlier: 4.056A pdb=" N PHE B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 removed outlier: 5.931A pdb=" N LEU B 244 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 264 removed outlier: 3.757A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.596A pdb=" N SER B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 removed outlier: 4.064A pdb=" N THR B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 removed outlier: 4.462A pdb=" N ARG B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 319' Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.503A pdb=" N ALA C 20 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 34 removed outlier: 4.075A pdb=" N LEU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 4.164A pdb=" N ALA C 61 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 62 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 63 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.883A pdb=" N CYS C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.657A pdb=" N ALA C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 204 through 211 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.731A pdb=" N GLN C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.754A pdb=" N PHE C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 4.563A pdb=" N ALA C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.645A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 308 removed outlier: 4.175A pdb=" N LYS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.917A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.697A pdb=" N LEU C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 5.051A pdb=" N GLU C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 346 " --> pdb=" O LYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 removed outlier: 3.703A pdb=" N ILE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 351' Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.735A pdb=" N ILE D 21 " --> pdb=" O PHE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 4.062A pdb=" N ASP D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 4.104A pdb=" N THR D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.620A pdb=" N LEU D 157 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.611A pdb=" N ASP D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 232 removed outlier: 4.294A pdb=" N GLN D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 247 through 263 removed outlier: 4.228A pdb=" N LYS D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.633A pdb=" N GLU D 267 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 removed outlier: 3.655A pdb=" N ILE D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 293 through 304 removed outlier: 4.028A pdb=" N ASN D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.994A pdb=" N ARG D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.575A pdb=" N VAL D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 removed outlier: 4.154A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 61 removed outlier: 3.510A pdb=" N ILE E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 61 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 4.071A pdb=" N GLN E 91 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 removed outlier: 3.673A pdb=" N VAL E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 168 through 173 removed outlier: 4.326A pdb=" N SER E 172 " --> pdb=" O ASP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 removed outlier: 3.553A pdb=" N ASP E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 239 Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 247 through 263 removed outlier: 3.775A pdb=" N GLN E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN E 255 " --> pdb=" O GLN E 251 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 removed outlier: 3.566A pdb=" N GLU E 267 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 268 " --> pdb=" O LEU E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 268' Processing helix chain 'E' and resid 271 through 283 removed outlier: 3.946A pdb=" N SER E 279 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL E 281 " --> pdb=" O LYS E 277 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 292 through 304 removed outlier: 3.892A pdb=" N THR E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS E 301 " --> pdb=" O ASN E 297 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 323 removed outlier: 3.623A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU E 323 " --> pdb=" O ARG E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 removed outlier: 3.528A pdb=" N LYS E 342 " --> pdb=" O ASP E 338 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 37 removed outlier: 3.520A pdb=" N ASP F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.932A pdb=" N ASP F 209 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 233 through 239 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 247 through 258 removed outlier: 3.537A pdb=" N GLN F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 268 removed outlier: 4.033A pdb=" N LEU F 265 " --> pdb=" O GLN F 262 " (cutoff:3.500A) Proline residue: F 266 - end of helix Processing helix chain 'F' and resid 271 through 278 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.643A pdb=" N LYS F 301 " --> pdb=" O ASN F 297 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 322 removed outlier: 3.938A pdb=" N THR F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.976A pdb=" N PHE F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.666A pdb=" N VAL A 177 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.887A pdb=" N VAL B 109 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP B 153 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 111 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 150 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 195 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 43 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N GLY B 196 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 45 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.738A pdb=" N GLU B 102 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.836A pdb=" N SER C 195 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 47 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET C 44 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE C 217 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET C 46 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.679A pdb=" N GLU C 102 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 108 through 110 removed outlier: 4.000A pdb=" N TYR D 151 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 150 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 195 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET D 44 " --> pdb=" O MET D 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 42 through 43 removed outlier: 7.645A pdb=" N GLY E 42 " --> pdb=" O MET E 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 151 removed outlier: 3.507A pdb=" N LEU E 150 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 193 " --> pdb=" O LEU E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 44 through 45 removed outlier: 6.948A pdb=" N MET F 44 " --> pdb=" O ALA F 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 149 through 150 396 hydrogen bonds defined for protein. 1077 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: 3.35 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3805 1.33 - 1.45: 2293 1.45 - 1.58: 8537 1.58 - 1.70: 29 1.70 - 1.82: 85 Bond restraints: 14749 Sorted by residual: bond pdb=" CB PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.68e+00 bond pdb=" CG LEU E 31 " pdb=" CD2 LEU E 31 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" C PRO F 240 " pdb=" N PRO F 241 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" CB ASP A 153 " pdb=" CG ASP A 153 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CG GLN F 228 " pdb=" CD GLN F 228 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 14744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 19778 2.74 - 5.49: 178 5.49 - 8.23: 30 8.23 - 10.97: 8 10.97 - 13.72: 3 Bond angle restraints: 19997 Sorted by residual: angle pdb=" N ILE D 184 " pdb=" CA ILE D 184 " pdb=" C ILE D 184 " ideal model delta sigma weight residual 111.91 106.51 5.40 8.90e-01 1.26e+00 3.68e+01 angle pdb=" C ARG D 185 " pdb=" N HIS D 186 " pdb=" CA HIS D 186 " ideal model delta sigma weight residual 120.49 127.92 -7.43 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CA PRO E 198 " pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 112.00 104.93 7.07 1.40e+00 5.10e-01 2.55e+01 angle pdb=" CB MET A 213 " pdb=" CG MET A 213 " pdb=" SD MET A 213 " ideal model delta sigma weight residual 112.70 126.42 -13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB MET A 44 " pdb=" CG MET A 44 " pdb=" SD MET A 44 " ideal model delta sigma weight residual 112.70 125.60 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 19992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 8526 31.14 - 62.29: 614 62.29 - 93.43: 53 93.43 - 124.57: 2 124.57 - 155.72: 1 Dihedral angle restraints: 9196 sinusoidal: 3939 harmonic: 5257 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.72 -155.72 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.15 -111.15 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 49.33 -109.33 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1388 0.031 - 0.062: 603 0.062 - 0.093: 223 0.093 - 0.124: 103 0.124 - 0.155: 12 Chirality restraints: 2329 Sorted by residual: chirality pdb=" CA ILE D 184 " pdb=" N ILE D 184 " pdb=" C ILE D 184 " pdb=" CB ILE D 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE E 337 " pdb=" N ILE E 337 " pdb=" C ILE E 337 " pdb=" CB ILE E 337 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ASN D 156 " pdb=" N ASN D 156 " pdb=" C ASN D 156 " pdb=" CB ASN D 156 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2326 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 197 " 0.045 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO E 198 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 198 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 198 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 233 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ARG C 233 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG C 233 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 204 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 205 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.029 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 224 2.62 - 3.19: 13192 3.19 - 3.76: 22324 3.76 - 4.33: 28074 4.33 - 4.90: 43888 Nonbonded interactions: 107702 Sorted by model distance: nonbonded pdb=" O1G ATP D 401 " pdb="MG MG D 402 " model vdw 2.045 2.170 nonbonded pdb=" O1G ATP A 401 " pdb="MG MG A 402 " model vdw 2.069 2.170 nonbonded pdb=" O1G ATP B 401 " pdb="MG MG B 402 " model vdw 2.074 2.170 nonbonded pdb=" O2B ATP E 401 " pdb="MG MG E 402 " model vdw 2.076 2.170 nonbonded pdb=" O1G ATP E 401 " pdb="MG MG E 402 " model vdw 2.080 2.170 ... (remaining 107697 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 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = chain 'D' selection = (chain 'E' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) } 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.230 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.003 0.119 14749 Z= 0.125 Angle : 0.696 13.716 19997 Z= 0.347 Chirality : 0.042 0.155 2329 Planarity : 0.004 0.065 2585 Dihedral : 19.450 155.717 5780 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.44 % Allowed : 40.06 % Favored : 59.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1793 helix: -0.42 (0.22), residues: 604 sheet: -0.82 (0.50), residues: 131 loop : -1.77 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 174 HIS 0.002 0.000 HIS F 214 PHE 0.020 0.001 PHE E 190 TYR 0.005 0.001 TYR D 306 ARG 0.007 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.25449 ( 396) hydrogen bonds : angle 7.47719 ( 1077) covalent geometry : bond 0.00277 (14749) covalent geometry : angle 0.69612 (19997) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: B 342 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: C 229 ILE cc_start: 0.9018 (pt) cc_final: 0.8790 (tp) REVERT: E 214 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8145 (t-90) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.2368 time to fit residues: 55.8569 Evaluate side-chains 148 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 214 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN ** F 34 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 = 0.3743 r_free = 0.3743 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081783 restraints weight = 56245.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083793 restraints weight = 34044.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085164 restraints weight = 24256.828| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14749 Z= 0.131 Angle : 0.627 11.539 19997 Z= 0.307 Chirality : 0.043 0.168 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.473 158.358 2162 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 5.27 % Allowed : 33.48 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1793 helix: -0.31 (0.21), residues: 653 sheet: -0.97 (0.43), residues: 175 loop : -1.90 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS D 186 PHE 0.013 0.001 PHE E 190 TYR 0.009 0.001 TYR F 306 ARG 0.004 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 396) hydrogen bonds : angle 5.39708 ( 1077) covalent geometry : bond 0.00296 (14749) covalent geometry : angle 0.62686 (19997) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 145 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7821 (tt) REVERT: A 44 MET cc_start: 0.8066 (tmm) cc_final: 0.7741 (tmm) REVERT: A 154 GLU cc_start: 0.8108 (pm20) cc_final: 0.7775 (pm20) REVERT: A 325 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8120 (tt) REVERT: D 206 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8796 (tp40) REVERT: E 214 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8181 (t-90) REVERT: E 315 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7265 (t0) outliers start: 84 outliers final: 42 residues processed: 214 average time/residue: 0.2350 time to fit residues: 77.7456 Evaluate side-chains 181 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 132 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 150 optimal weight: 0.0870 chunk 2 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 186 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 239 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** F 34 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 = 0.3744 r_free = 0.3744 target = 0.100200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.082040 restraints weight = 56242.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084071 restraints weight = 33732.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085445 restraints weight = 23988.071| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14749 Z= 0.118 Angle : 0.618 11.461 19997 Z= 0.299 Chirality : 0.043 0.274 2329 Planarity : 0.004 0.052 2585 Dihedral : 11.165 159.596 2158 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 5.20 % Allowed : 33.10 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1793 helix: -0.28 (0.21), residues: 649 sheet: -1.45 (0.46), residues: 144 loop : -1.88 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS C 327 PHE 0.013 0.001 PHE C 75 TYR 0.008 0.001 TYR F 306 ARG 0.003 0.000 ARG F 326 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 396) hydrogen bonds : angle 5.10785 ( 1077) covalent geometry : bond 0.00269 (14749) covalent geometry : angle 0.61798 (19997) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 144 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8207 (tmm) cc_final: 0.7510 (tmm) REVERT: A 153 ASP cc_start: 0.8284 (p0) cc_final: 0.8054 (p0) REVERT: B 207 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7370 (tt) REVERT: C 75 PHE cc_start: 0.6559 (OUTLIER) cc_final: 0.6239 (t80) REVERT: D 206 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8753 (tp40) REVERT: E 270 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8369 (tt) REVERT: E 315 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7253 (t0) REVERT: E 330 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6418 (tpp-160) outliers start: 83 outliers final: 54 residues processed: 212 average time/residue: 0.2224 time to fit residues: 73.9183 Evaluate side-chains 199 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 0.0870 chunk 134 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 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 = 0.3753 r_free = 0.3753 target = 0.100659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082457 restraints weight = 56135.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084484 restraints weight = 33412.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085875 restraints weight = 23674.010| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14749 Z= 0.111 Angle : 0.613 11.747 19997 Z= 0.295 Chirality : 0.043 0.242 2329 Planarity : 0.004 0.049 2585 Dihedral : 10.874 158.542 2154 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 5.27 % Allowed : 32.98 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1793 helix: -0.22 (0.21), residues: 664 sheet: -1.41 (0.45), residues: 149 loop : -1.87 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS C 327 PHE 0.014 0.001 PHE E 190 TYR 0.008 0.001 TYR F 306 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 396) hydrogen bonds : angle 4.87014 ( 1077) covalent geometry : bond 0.00255 (14749) covalent geometry : angle 0.61267 (19997) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 151 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8393 (p0) cc_final: 0.8177 (p0) REVERT: A 154 GLU cc_start: 0.8175 (pm20) cc_final: 0.7728 (pm20) REVERT: B 27 MET cc_start: 0.8076 (tmm) cc_final: 0.7785 (tmm) REVERT: B 207 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7386 (tt) REVERT: B 311 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: C 75 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.6222 (t80) REVERT: D 206 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8720 (tp40) REVERT: E 167 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7947 (tp) REVERT: E 270 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8352 (tt) REVERT: E 315 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7310 (t0) REVERT: E 330 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6374 (tpp-160) REVERT: F 189 ARG cc_start: 0.6332 (mmp80) cc_final: 0.5641 (ptt180) REVERT: F 238 GLN cc_start: 0.9088 (mm110) cc_final: 0.8498 (tm-30) outliers start: 84 outliers final: 57 residues processed: 224 average time/residue: 0.2078 time to fit residues: 73.4220 Evaluate side-chains 212 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 147 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 19 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.098048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079947 restraints weight = 57358.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081900 restraints weight = 34685.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083230 restraints weight = 24786.752| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14749 Z= 0.159 Angle : 0.653 10.842 19997 Z= 0.318 Chirality : 0.044 0.157 2329 Planarity : 0.004 0.051 2585 Dihedral : 11.234 151.518 2154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 6.65 % Allowed : 32.29 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1793 helix: -0.23 (0.20), residues: 655 sheet: -1.69 (0.43), residues: 155 loop : -1.98 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.005 0.001 HIS C 327 PHE 0.013 0.001 PHE F 18 TYR 0.016 0.001 TYR B 341 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 396) hydrogen bonds : angle 5.06771 ( 1077) covalent geometry : bond 0.00364 (14749) covalent geometry : angle 0.65260 (19997) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 140 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8280 (tmm) cc_final: 0.7700 (tmm) REVERT: A 153 ASP cc_start: 0.8496 (p0) cc_final: 0.8214 (p0) REVERT: A 154 GLU cc_start: 0.8283 (pm20) cc_final: 0.7842 (pm20) REVERT: A 267 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 291 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7844 (ttt-90) REVERT: B 311 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: C 75 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6539 (t80) REVERT: D 85 MET cc_start: 0.6671 (mmm) cc_final: 0.6321 (mmm) REVERT: E 270 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (tt) REVERT: E 315 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7369 (t0) REVERT: E 330 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6412 (tpp-160) REVERT: F 286 ASP cc_start: 0.8530 (t0) cc_final: 0.8248 (t0) outliers start: 106 outliers final: 74 residues processed: 232 average time/residue: 0.2215 time to fit residues: 80.3342 Evaluate side-chains 217 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 136 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 67 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081558 restraints weight = 58116.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.083416 restraints weight = 36254.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084690 restraints weight = 26322.890| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14749 Z= 0.138 Angle : 0.652 11.308 19997 Z= 0.316 Chirality : 0.043 0.157 2329 Planarity : 0.004 0.049 2585 Dihedral : 11.096 149.749 2154 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 6.21 % Allowed : 33.23 % Favored : 60.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.20), residues: 1793 helix: -0.17 (0.21), residues: 655 sheet: -1.20 (0.43), residues: 166 loop : -2.08 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.007 0.001 HIS C 214 PHE 0.012 0.001 PHE F 18 TYR 0.011 0.001 TYR F 306 ARG 0.004 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 396) hydrogen bonds : angle 5.00639 ( 1077) covalent geometry : bond 0.00319 (14749) covalent geometry : angle 0.65171 (19997) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 139 time to evaluate : 1.802 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8388 (p0) cc_final: 0.8183 (p0) REVERT: A 154 GLU cc_start: 0.8209 (pm20) cc_final: 0.7713 (pm20) REVERT: A 267 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: B 291 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7793 (ttt-90) REVERT: B 311 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: C 75 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6535 (t80) REVERT: C 272 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8199 (t80) REVERT: D 85 MET cc_start: 0.6658 (mmm) cc_final: 0.6284 (mmm) REVERT: D 151 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6638 (p90) REVERT: E 315 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7293 (t0) REVERT: E 330 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6273 (tpp-160) REVERT: F 34 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8913 (m-40) REVERT: F 286 ASP cc_start: 0.8489 (t0) cc_final: 0.8202 (t0) outliers start: 99 outliers final: 80 residues processed: 223 average time/residue: 0.2171 time to fit residues: 76.0465 Evaluate side-chains 224 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 135 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 127 optimal weight: 0.0770 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081942 restraints weight = 57681.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083805 restraints weight = 35822.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085082 restraints weight = 25990.258| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14749 Z= 0.128 Angle : 0.646 11.082 19997 Z= 0.311 Chirality : 0.043 0.153 2329 Planarity : 0.004 0.048 2585 Dihedral : 10.860 139.216 2154 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 6.33 % Allowed : 33.48 % Favored : 60.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1793 helix: -0.12 (0.21), residues: 658 sheet: -1.52 (0.45), residues: 146 loop : -2.00 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.004 0.001 HIS C 327 PHE 0.011 0.001 PHE F 18 TYR 0.010 0.001 TYR F 306 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 396) hydrogen bonds : angle 4.87827 ( 1077) covalent geometry : bond 0.00296 (14749) covalent geometry : angle 0.64616 (19997) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 144 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8098 (tmm) cc_final: 0.7531 (tmm) REVERT: A 153 ASP cc_start: 0.8378 (p0) cc_final: 0.8156 (p0) REVERT: A 154 GLU cc_start: 0.8272 (pm20) cc_final: 0.7795 (pm20) REVERT: A 267 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 207 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 291 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7789 (ttt-90) REVERT: B 311 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: C 75 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6500 (t80) REVERT: C 272 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8190 (t80) REVERT: D 85 MET cc_start: 0.6693 (mmm) cc_final: 0.6343 (mmm) REVERT: D 151 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6622 (p90) REVERT: D 206 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8790 (tp40) REVERT: E 315 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7351 (t0) REVERT: E 330 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6290 (tpp-160) REVERT: F 34 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8915 (m-40) REVERT: F 242 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8432 (m) REVERT: F 286 ASP cc_start: 0.8527 (t0) cc_final: 0.8228 (t0) outliers start: 101 outliers final: 77 residues processed: 231 average time/residue: 0.2242 time to fit residues: 81.2648 Evaluate side-chains 229 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 140 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** 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 = 0.3750 r_free = 0.3750 target = 0.099035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081401 restraints weight = 57412.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083271 restraints weight = 35986.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084545 restraints weight = 26126.972| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14749 Z= 0.155 Angle : 0.673 11.366 19997 Z= 0.326 Chirality : 0.043 0.165 2329 Planarity : 0.004 0.049 2585 Dihedral : 11.008 128.676 2154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 6.46 % Allowed : 33.98 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.20), residues: 1793 helix: -0.21 (0.20), residues: 664 sheet: -1.60 (0.44), residues: 146 loop : -2.07 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.011 0.001 HIS A 214 PHE 0.016 0.001 PHE E 190 TYR 0.013 0.001 TYR F 306 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 396) hydrogen bonds : angle 5.04237 ( 1077) covalent geometry : bond 0.00356 (14749) covalent geometry : angle 0.67271 (19997) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 140 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8134 (tmm) cc_final: 0.7654 (tmm) REVERT: A 153 ASP cc_start: 0.8450 (p0) cc_final: 0.8150 (p0) REVERT: A 154 GLU cc_start: 0.8353 (pm20) cc_final: 0.7828 (pm20) REVERT: A 267 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: B 207 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7530 (tt) REVERT: B 291 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7913 (ttt-90) REVERT: B 311 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: C 75 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6622 (t80) REVERT: C 272 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8116 (t80) REVERT: D 85 MET cc_start: 0.6700 (mmm) cc_final: 0.6323 (mmm) REVERT: D 151 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6708 (p90) REVERT: E 315 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7385 (t0) REVERT: E 330 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6232 (tpp-160) REVERT: F 34 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8943 (m-40) REVERT: F 242 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8372 (m) REVERT: F 286 ASP cc_start: 0.8468 (t0) cc_final: 0.8165 (t0) outliers start: 103 outliers final: 84 residues processed: 228 average time/residue: 0.2210 time to fit residues: 79.5897 Evaluate side-chains 233 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 138 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** 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 = 0.3763 r_free = 0.3763 target = 0.100110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082544 restraints weight = 57381.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084460 restraints weight = 35399.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085798 restraints weight = 25540.116| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14749 Z= 0.117 Angle : 0.656 12.918 19997 Z= 0.314 Chirality : 0.043 0.157 2329 Planarity : 0.004 0.049 2585 Dihedral : 10.681 125.474 2154 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 5.45 % Allowed : 35.30 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1793 helix: -0.05 (0.21), residues: 665 sheet: -1.42 (0.44), residues: 152 loop : -1.99 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.009 0.001 HIS A 214 PHE 0.012 0.001 PHE A 190 TYR 0.009 0.001 TYR F 306 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 396) hydrogen bonds : angle 4.81506 ( 1077) covalent geometry : bond 0.00268 (14749) covalent geometry : angle 0.65619 (19997) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 145 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8030 (tmm) cc_final: 0.7465 (tmm) REVERT: A 153 ASP cc_start: 0.8403 (p0) cc_final: 0.8170 (p0) REVERT: A 154 GLU cc_start: 0.8252 (pm20) cc_final: 0.7760 (pm20) REVERT: B 207 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7504 (tt) REVERT: B 311 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7552 (pp20) REVERT: C 75 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6342 (t80) REVERT: C 272 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8066 (t80) REVERT: D 85 MET cc_start: 0.6634 (mmm) cc_final: 0.6285 (mmm) REVERT: D 151 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6545 (p90) REVERT: D 211 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6576 (t80) REVERT: E 315 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7362 (t0) REVERT: E 330 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6183 (tpp-160) REVERT: F 34 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8901 (m-40) REVERT: F 242 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8355 (m) REVERT: F 286 ASP cc_start: 0.8556 (t0) cc_final: 0.8281 (t0) outliers start: 87 outliers final: 72 residues processed: 217 average time/residue: 0.2324 time to fit residues: 79.4995 Evaluate side-chains 223 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 141 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 76 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.100144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082497 restraints weight = 57698.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084419 restraints weight = 35744.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085760 restraints weight = 25730.836| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14749 Z= 0.119 Angle : 0.660 13.494 19997 Z= 0.315 Chirality : 0.043 0.158 2329 Planarity : 0.004 0.049 2585 Dihedral : 10.548 131.000 2154 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 5.58 % Allowed : 35.49 % Favored : 58.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1793 helix: 0.04 (0.21), residues: 658 sheet: -1.41 (0.44), residues: 152 loop : -1.94 (0.21), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.008 0.001 HIS C 214 PHE 0.019 0.001 PHE E 190 TYR 0.009 0.001 TYR F 306 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 396) hydrogen bonds : angle 4.79384 ( 1077) covalent geometry : bond 0.00274 (14749) covalent geometry : angle 0.66038 (19997) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 141 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8017 (tmm) cc_final: 0.7438 (tmm) REVERT: A 153 ASP cc_start: 0.8420 (p0) cc_final: 0.8201 (p0) REVERT: A 154 GLU cc_start: 0.8252 (pm20) cc_final: 0.7785 (pm20) REVERT: B 207 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7500 (tt) REVERT: B 311 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: C 75 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6310 (t80) REVERT: C 272 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8010 (t80) REVERT: D 85 MET cc_start: 0.6584 (mmm) cc_final: 0.6219 (mmm) REVERT: D 151 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6628 (p90) REVERT: D 206 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8734 (tp40) REVERT: D 211 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6464 (t80) REVERT: E 33 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9085 (mm) REVERT: E 315 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7373 (t0) REVERT: E 330 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6234 (tpp-160) REVERT: F 34 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8940 (m-40) REVERT: F 242 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (m) REVERT: F 286 ASP cc_start: 0.8548 (t0) cc_final: 0.8268 (t0) outliers start: 89 outliers final: 73 residues processed: 218 average time/residue: 0.2121 time to fit residues: 73.8146 Evaluate side-chains 226 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 141 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 147 optimal weight: 2.9990 chunk 98 optimal weight: 0.0060 chunk 108 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS B 72 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 HIS ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.099896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082234 restraints weight = 57324.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.084153 restraints weight = 35188.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.085476 restraints weight = 25286.732| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14749 Z= 0.142 Angle : 0.679 13.538 19997 Z= 0.325 Chirality : 0.043 0.163 2329 Planarity : 0.004 0.048 2585 Dihedral : 10.629 139.123 2154 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 5.77 % Allowed : 35.49 % Favored : 58.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.20), residues: 1793 helix: -0.00 (0.21), residues: 658 sheet: -1.53 (0.44), residues: 151 loop : -2.00 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.007 0.001 HIS E 327 PHE 0.012 0.001 PHE A 190 TYR 0.011 0.001 TYR F 306 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 396) hydrogen bonds : angle 4.87147 ( 1077) covalent geometry : bond 0.00329 (14749) covalent geometry : angle 0.67950 (19997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.57 seconds wall clock time: 77 minutes 15.40 seconds (4635.40 seconds total)