Starting phenix.real_space_refine on Sun Oct 13 11:08:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_17151.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_17151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_17151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_17151.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/10_2024/8osf_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-5477/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: 9.57, per 1000 atoms: 0.66 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: 3.95 Conformation dependent library (CDL) restraints added in 2.0 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: 1.50 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: 3.79 Time building geometry restraints manager: 4.26 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.880 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- 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= 0.176 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.679 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: 0.2448 time to fit residues: 57.5493 Evaluate side-chains 148 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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= 0.192 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 *********************** 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 fitting. rotamer outliers: 84 poor density : 145 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7801 (tt) REVERT: A 44 MET cc_start: 0.8089 (tmm) cc_final: 0.7760 (tmm) REVERT: A 154 GLU cc_start: 0.8114 (pm20) cc_final: 0.7785 (pm20) REVERT: A 325 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 206 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8792 (tp40) REVERT: E 214 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8181 (t-90) REVERT: E 315 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7266 (t0) outliers start: 84 outliers final: 42 residues processed: 214 average time/residue: 0.2436 time to fit residues: 79.8292 Evaluate side-chains 181 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 134 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 0.0470 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 107 GLN C 239 ASN D 76 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14749 Z= 0.155 Angle : 0.613 11.621 19997 Z= 0.295 Chirality : 0.042 0.250 2329 Planarity : 0.004 0.052 2585 Dihedral : 11.004 160.160 2158 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.39 % Allowed : 33.42 % Favored : 62.19 % 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: -1.74 (0.20), residues: 1793 helix: -0.26 (0.21), residues: 650 sheet: -0.82 (0.47), residues: 144 loop : -1.88 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS A 214 PHE 0.012 0.001 PHE C 75 TYR 0.007 0.001 TYR D 306 ARG 0.003 0.000 ARG A 49 *********************** 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 fitting. rotamer outliers: 70 poor density : 157 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8175 (tmm) cc_final: 0.7484 (tmm) REVERT: A 153 ASP cc_start: 0.8216 (p0) cc_final: 0.8014 (p0) REVERT: A 325 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 27 MET cc_start: 0.8061 (tmm) cc_final: 0.7765 (tmm) REVERT: B 311 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: C 46 MET cc_start: 0.7139 (mmt) cc_final: 0.6626 (mmp) REVERT: C 75 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.6053 (t80) REVERT: D 206 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (tp40) REVERT: E 34 ASN cc_start: 0.8102 (p0) cc_final: 0.7738 (t0) REVERT: E 270 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (tt) REVERT: E 315 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7202 (t0) REVERT: E 330 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6361 (tpp-160) REVERT: F 199 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: F 238 GLN cc_start: 0.9118 (mm110) cc_final: 0.8594 (tm-30) REVERT: F 255 GLN cc_start: 0.7414 (pt0) cc_final: 0.7212 (tm-30) outliers start: 70 outliers final: 44 residues processed: 214 average time/residue: 0.2312 time to fit residues: 76.8713 Evaluate side-chains 206 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 154 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 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 A residue 325 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN 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 208 LEU Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 267 GLU 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 108 MET 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 45 ILE Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 242 THR 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 162 optimal weight: 4.9990 chunk 123 optimal weight: 0.0870 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN D 228 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1631 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= 0.214 Angle : 0.632 10.936 19997 Z= 0.307 Chirality : 0.043 0.235 2329 Planarity : 0.004 0.051 2585 Dihedral : 11.022 155.631 2154 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 5.83 % Allowed : 32.60 % Favored : 61.57 % 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 (0.20), residues: 1793 helix: -0.21 (0.21), residues: 658 sheet: -1.16 (0.43), residues: 170 loop : -1.95 (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 C 327 PHE 0.014 0.001 PHE E 190 TYR 0.011 0.001 TYR F 306 ARG 0.003 0.000 ARG A 179 *********************** 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 238 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 145 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8394 (p0) cc_final: 0.8177 (p0) REVERT: A 154 GLU cc_start: 0.8203 (pm20) cc_final: 0.7755 (pm20) REVERT: C 75 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6408 (t80) REVERT: C 272 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8447 (t80) REVERT: E 270 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8395 (tt) REVERT: E 315 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7332 (t0) REVERT: E 330 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6367 (tpp-160) REVERT: F 46 MET cc_start: 0.6210 (tpt) cc_final: 0.5725 (tpt) REVERT: F 199 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: F 286 ASP cc_start: 0.8501 (t0) cc_final: 0.8228 (t0) outliers start: 93 outliers final: 64 residues processed: 221 average time/residue: 0.2316 time to fit residues: 79.3712 Evaluate side-chains 213 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 143 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 LEU 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 22 VAL 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 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN 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 208 LEU Chi-restraints excluded: chain C residue 263 LYS 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 77 SER 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 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 40 ILE Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 199 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 214 HIS ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1813 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= 0.216 Angle : 0.640 11.204 19997 Z= 0.312 Chirality : 0.043 0.147 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.135 150.756 2152 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 6.27 % Allowed : 32.60 % Favored : 61.13 % 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: -0.21 (0.21), residues: 655 sheet: -1.64 (0.43), residues: 155 loop : -1.95 (0.21), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.004 0.001 HIS C 327 PHE 0.012 0.001 PHE A 190 TYR 0.012 0.001 TYR F 306 ARG 0.003 0.000 ARG B 49 *********************** 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 245 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 145 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8458 (p0) cc_final: 0.8192 (p0) REVERT: A 154 GLU cc_start: 0.8241 (pm20) cc_final: 0.7807 (pm20) REVERT: A 267 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: B 291 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7748 (ttt-90) REVERT: B 311 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: C 75 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6586 (t80) REVERT: C 272 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8394 (t80) REVERT: D 206 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8792 (tp40) REVERT: E 270 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8410 (tt) REVERT: E 315 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7327 (t0) REVERT: E 330 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6371 (tpp-160) REVERT: F 199 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: F 286 ASP cc_start: 0.8519 (t0) cc_final: 0.8224 (t0) outliers start: 100 outliers final: 69 residues processed: 229 average time/residue: 0.2457 time to fit residues: 87.1094 Evaluate side-chains 219 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 140 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL 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 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR 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 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 263 LYS 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 67 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 206 GLN Chi-restraints excluded: chain D residue 281 VAL 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 199 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 10.0000 chunk 157 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 0.0030 overall best weight: 1.2192 ------------------------------------------------------------------------------- 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** ** B 91 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 ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1861 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= 0.171 Angle : 0.624 11.399 19997 Z= 0.301 Chirality : 0.043 0.144 2329 Planarity : 0.004 0.050 2585 Dihedral : 10.770 140.974 2152 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 5.83 % Allowed : 32.98 % Favored : 61.19 % 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: -1.77 (0.20), residues: 1793 helix: -0.12 (0.21), residues: 657 sheet: -1.39 (0.45), residues: 146 loop : -1.93 (0.20), residues: 990 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 C 75 TYR 0.008 0.001 TYR F 306 ARG 0.003 0.000 ARG C 326 *********************** 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 242 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 149 time to evaluate : 1.883 Fit side-chains revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8439 (p0) cc_final: 0.8177 (p0) REVERT: A 154 GLU cc_start: 0.8215 (pm20) cc_final: 0.7726 (pm20) REVERT: B 311 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: C 75 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6461 (t80) REVERT: C 263 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7612 (mmmm) REVERT: C 272 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8355 (t80) REVERT: D 206 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8732 (tp40) REVERT: E 34 ASN cc_start: 0.8276 (p0) cc_final: 0.7585 (t0) REVERT: E 270 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8411 (tt) REVERT: E 315 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7377 (t0) REVERT: E 330 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6356 (tpp-160) REVERT: F 34 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8869 (m-40) REVERT: F 46 MET cc_start: 0.6108 (tpt) cc_final: 0.5744 (tpt) REVERT: F 199 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6664 (tt0) REVERT: F 286 ASP cc_start: 0.8487 (t0) cc_final: 0.8168 (t0) outliers start: 93 outliers final: 67 residues processed: 225 average time/residue: 0.2549 time to fit residues: 88.3089 Evaluate side-chains 223 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 146 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 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 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 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR 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 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 263 LYS 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 327 HIS Chi-restraints excluded: chain D residue 32 LEU 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 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 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 108 MET 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 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 34 ASN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 199 GLU 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 255 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 127 optimal weight: 0.0970 chunk 147 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B 91 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** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 14749 Z= 0.161 Angle : 0.633 11.466 19997 Z= 0.303 Chirality : 0.042 0.165 2329 Planarity : 0.004 0.051 2585 Dihedral : 10.430 121.956 2152 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 4.95 % Allowed : 33.98 % 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: -1.68 (0.20), residues: 1793 helix: -0.09 (0.21), residues: 672 sheet: -1.15 (0.48), residues: 131 loop : -1.89 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.015 0.001 HIS C 214 PHE 0.018 0.001 PHE E 190 TYR 0.020 0.001 TYR B 341 ARG 0.004 0.000 ARG A 49 *********************** 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 237 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 158 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8188 (tmm) cc_final: 0.7630 (tmm) REVERT: A 153 ASP cc_start: 0.8461 (p0) cc_final: 0.8229 (p0) REVERT: A 154 GLU cc_start: 0.8236 (pm20) cc_final: 0.7801 (pm20) REVERT: B 311 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: C 75 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6200 (t80) REVERT: D 197 ASN cc_start: 0.7336 (t0) cc_final: 0.7102 (t0) REVERT: D 206 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8678 (tp40) REVERT: D 262 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: E 270 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8388 (tt) REVERT: E 315 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7435 (t0) REVERT: E 330 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6306 (tpp-160) REVERT: F 34 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8868 (m-40) REVERT: F 199 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: F 286 ASP cc_start: 0.8456 (t0) cc_final: 0.8117 (t0) REVERT: F 326 ARG cc_start: 0.6865 (tpt90) cc_final: 0.6399 (mmm160) outliers start: 79 outliers final: 62 residues processed: 222 average time/residue: 0.2447 time to fit residues: 86.0116 Evaluate side-chains 221 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 150 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 150 LEU Chi-restraints excluded: chain A residue 163 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 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 176 THR Chi-restraints excluded: chain B residue 186 HIS 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 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE 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 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 262 GLN Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 108 MET 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 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 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 199 GLU Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 255 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN D 175 ASN E 327 HIS ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14749 Z= 0.160 Angle : 0.642 11.799 19997 Z= 0.304 Chirality : 0.042 0.151 2329 Planarity : 0.004 0.051 2585 Dihedral : 10.059 136.100 2152 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.02 % Allowed : 34.61 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1793 helix: 0.12 (0.21), residues: 652 sheet: -0.87 (0.44), residues: 156 loop : -1.87 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.009 0.001 HIS A 214 PHE 0.010 0.001 PHE C 75 TYR 0.006 0.001 TYR F 306 ARG 0.003 0.000 ARG A 49 *********************** 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 238 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 158 time to evaluate : 1.732 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8010 (tmm) cc_final: 0.7525 (tmm) REVERT: A 153 ASP cc_start: 0.8462 (p0) cc_final: 0.8252 (p0) REVERT: A 154 GLU cc_start: 0.8236 (pm20) cc_final: 0.7782 (pm20) REVERT: B 311 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: C 75 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.6072 (t80) REVERT: C 263 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7654 (mmmm) REVERT: D 211 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6275 (t80) REVERT: E 270 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (tt) REVERT: E 330 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6309 (tpp-160) REVERT: F 34 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8875 (m-40) REVERT: F 46 MET cc_start: 0.5817 (tpt) cc_final: 0.5439 (tpt) REVERT: F 199 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: F 286 ASP cc_start: 0.8484 (t0) cc_final: 0.8143 (t0) REVERT: F 326 ARG cc_start: 0.6776 (tpt90) cc_final: 0.6319 (mmm160) outliers start: 80 outliers final: 63 residues processed: 223 average time/residue: 0.2505 time to fit residues: 86.6710 Evaluate side-chains 220 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 149 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 45 ILE 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 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 176 THR Chi-restraints excluded: chain B residue 186 HIS 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 34 ASN 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 220 VAL Chi-restraints excluded: chain C residue 263 LYS 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 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 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 211 PHE Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain E residue 108 MET 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 270 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR 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 63 LEU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 211 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 127 optimal weight: 0.0470 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 overall best weight: 1.3660 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14749 Z= 0.180 Angle : 0.654 12.678 19997 Z= 0.311 Chirality : 0.043 0.158 2329 Planarity : 0.004 0.050 2585 Dihedral : 10.105 136.583 2152 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.95 % Allowed : 34.98 % Favored : 60.06 % 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: -1.52 (0.21), residues: 1793 helix: 0.13 (0.21), residues: 662 sheet: -1.04 (0.45), residues: 146 loop : -1.87 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 174 HIS 0.008 0.001 HIS A 214 PHE 0.019 0.001 PHE E 190 TYR 0.012 0.001 TYR B 341 ARG 0.002 0.000 ARG A 49 *********************** 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 224 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 145 time to evaluate : 1.628 Fit side-chains REVERT: A 44 MET cc_start: 0.8162 (tmm) cc_final: 0.7604 (tmm) REVERT: A 153 ASP cc_start: 0.8459 (p0) cc_final: 0.8232 (p0) REVERT: A 154 GLU cc_start: 0.8265 (pm20) cc_final: 0.7804 (pm20) REVERT: B 311 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: C 75 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5953 (t80) REVERT: C 263 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7688 (mmmm) REVERT: D 211 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6283 (t80) REVERT: E 270 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (tt) REVERT: E 330 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6265 (tpp-160) REVERT: F 34 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8901 (m-40) REVERT: F 46 MET cc_start: 0.5957 (tpt) cc_final: 0.5623 (tpt) REVERT: F 286 ASP cc_start: 0.8494 (t0) cc_final: 0.8152 (t0) REVERT: F 326 ARG cc_start: 0.6813 (tpt90) cc_final: 0.6345 (mmm160) outliers start: 79 outliers final: 66 residues processed: 209 average time/residue: 0.2341 time to fit residues: 76.3983 Evaluate side-chains 218 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 145 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 176 THR Chi-restraints excluded: chain B residue 186 HIS 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 220 VAL Chi-restraints excluded: chain C residue 263 LYS 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 67 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 106 VAL 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 211 PHE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 108 MET 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 227 VAL 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 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 211 PHE 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 104 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 119 optimal weight: 0.0370 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 0.0040 chunk 152 optimal weight: 10.0000 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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** B 72 ASN ** B 91 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** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 14749 Z= 0.162 Angle : 0.654 13.578 19997 Z= 0.310 Chirality : 0.042 0.153 2329 Planarity : 0.004 0.051 2585 Dihedral : 9.858 132.340 2152 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.26 % Allowed : 35.67 % Favored : 60.06 % 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: -1.44 (0.21), residues: 1793 helix: 0.18 (0.21), residues: 656 sheet: -0.73 (0.43), residues: 161 loop : -1.86 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 174 HIS 0.008 0.001 HIS A 214 PHE 0.010 0.001 PHE C 75 TYR 0.006 0.001 TYR F 341 ARG 0.003 0.000 ARG A 49 ********************** 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 223 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 155 time to evaluate : 1.897 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8038 (tmm) cc_final: 0.7507 (tmm) REVERT: A 154 GLU cc_start: 0.8213 (pm20) cc_final: 0.7769 (pm20) REVERT: B 311 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: C 75 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5849 (t80) REVERT: D 77 SER cc_start: 0.5953 (OUTLIER) cc_final: 0.5497 (p) REVERT: D 151 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6754 (p90) REVERT: D 211 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6101 (t80) REVERT: D 262 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.6739 (mt0) REVERT: E 270 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8407 (tt) REVERT: E 330 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6239 (tpp-160) REVERT: F 34 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8844 (m-40) REVERT: F 44 MET cc_start: 0.7260 (ppp) cc_final: 0.6708 (ppp) REVERT: F 46 MET cc_start: 0.5879 (tpt) cc_final: 0.5529 (tpt) REVERT: F 286 ASP cc_start: 0.8473 (t0) cc_final: 0.8109 (t0) REVERT: F 326 ARG cc_start: 0.6804 (tpt90) cc_final: 0.6361 (mmm160) outliers start: 68 outliers final: 56 residues processed: 209 average time/residue: 0.2594 time to fit residues: 84.3494 Evaluate side-chains 216 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 151 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 150 LEU Chi-restraints excluded: chain A residue 163 VAL 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 B residue 15 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 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 320 VAL 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 177 VAL Chi-restraints excluded: chain C residue 208 LEU 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 327 HIS 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 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 108 MET 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 227 VAL 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 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 45 ILE Chi-restraints excluded: chain F residue 211 PHE 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 43 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.100301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082683 restraints weight = 57724.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084576 restraints weight = 35867.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085881 restraints weight = 25932.280| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2248 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= 0.210 Angle : 0.679 13.797 19997 Z= 0.324 Chirality : 0.043 0.162 2329 Planarity : 0.004 0.049 2585 Dihedral : 10.204 135.956 2152 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 4.26 % Allowed : 35.67 % Favored : 60.06 % 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: -1.53 (0.21), residues: 1793 helix: 0.12 (0.21), residues: 660 sheet: -0.84 (0.43), residues: 162 loop : -1.92 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 174 HIS 0.006 0.001 HIS A 214 PHE 0.020 0.001 PHE E 190 TYR 0.020 0.001 TYR B 341 ARG 0.003 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2597.80 seconds wall clock time: 51 minutes 45.60 seconds (3105.60 seconds total)