Starting phenix.real_space_refine on Fri Aug 7 22:51:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hh5_34752/08_2026/8hh5_34752.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24277 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.41, per 1000 atoms: 0.18 Number of scatterers: 24277 At special positions: 0 Unit cell: (125.84, 124.96, 152.24, 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 77 16.00 P 18 15.00 Mg 6 11.99 O 4670 8.00 N 4219 7.00 C 15287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 985.8 milliseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 21 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.076A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.863A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.579A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.565A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.617A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.582A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.886A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.522A pdb=" N ALA A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 406 through 421 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.550A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.668A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.684A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.576A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.615A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.779A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.720A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 396 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.642A pdb=" N ILE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.837A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 486 through 498 removed outlier: 4.038A pdb=" N ALA B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.526A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.665A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.683A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 4.565A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 4.182A pdb=" N GLN C 397 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.517A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.647A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.609A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.597A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 180 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.598A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.656A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.173A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.536A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 378 Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.627A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.947A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.563A pdb=" N ARG D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.980A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 227 through 243 removed outlier: 3.842A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 4.036A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.576A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.051A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.695A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.686A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.543A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.061A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.504A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.633A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.509A pdb=" N GLY F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 removed outlier: 3.509A pdb=" N LEU F 392 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 392' Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.675A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.863A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.543A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.928A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 4.172A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.534A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.624A pdb=" N LEU G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 4.144A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 161 removed outlier: 3.995A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 3.979A pdb=" N GLN G 267 " --> pdb=" O ASN G 263 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.986A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.074A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.324A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.182A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.910A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.619A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.475A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.904A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.556A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.497A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.332A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN D 217 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.399A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.186A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.518A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.667A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.305A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 9.189A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 173 through 175 1157 hydrogen bonds defined for protein. 3291 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: 3.40 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8233 1.34 - 1.46: 3836 1.46 - 1.58: 12434 1.58 - 1.69: 27 1.69 - 1.81: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.506 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" CA VAL G 73 " pdb=" CB VAL G 73 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.18e+00 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 32972 2.03 - 4.05: 453 4.05 - 6.08: 50 6.08 - 8.10: 3 8.10 - 10.13: 1 Bond angle restraints: 33479 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 111.91 106.58 5.33 8.90e-01 1.26e+00 3.59e+01 angle pdb=" C ASN E 97 " pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 121.97 132.10 -10.13 1.80e+00 3.09e-01 3.16e+01 angle pdb=" N VAL B 366 " pdb=" CA VAL B 366 " pdb=" C VAL B 366 " ideal model delta sigma weight residual 113.42 108.65 4.77 1.17e+00 7.31e-01 1.66e+01 angle pdb=" N VAL E 98 " pdb=" CA VAL E 98 " pdb=" CB VAL E 98 " ideal model delta sigma weight residual 111.23 116.95 -5.72 1.65e+00 3.67e-01 1.20e+01 angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 107.32 112.98 -5.66 1.65e+00 3.67e-01 1.18e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 14626 33.41 - 66.82: 269 66.82 - 100.23: 41 100.23 - 133.64: 0 133.64 - 167.05: 2 Dihedral angle restraints: 14938 sinusoidal: 6013 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PA ADP D 603 " pdb=" PB ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 107.05 -167.05 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual 300.00 133.97 166.03 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA LEU G 159 " pdb=" C LEU G 159 " pdb=" N PHE G 160 " pdb=" CA PHE G 160 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 14935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2279 0.031 - 0.063: 998 0.063 - 0.094: 341 0.094 - 0.126: 208 0.126 - 0.157: 30 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA VAL E 214 " pdb=" N VAL E 214 " pdb=" C VAL E 214 " pdb=" CB VAL E 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB THR F 301 " pdb=" CA THR F 301 " pdb=" OG1 THR F 301 " pdb=" CG2 THR F 301 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL E 456 " pdb=" N VAL E 456 " pdb=" C VAL E 456 " pdb=" CB VAL E 456 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 43 " 0.067 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO G 44 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO G 44 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO G 44 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO F 221 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO E 316 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.023 5.00e-02 4.00e+02 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 91 2.48 - 3.09: 17027 3.09 - 3.69: 35678 3.69 - 4.30: 53451 4.30 - 4.90: 90894 Nonbonded interactions: 197141 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O4 PO4 D 602 " model vdw 1.881 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.943 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.005 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.008 2.170 ... (remaining 197136 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 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24684 Z= 0.163 Angle : 0.603 10.126 33479 Z= 0.346 Chirality : 0.045 0.157 3856 Planarity : 0.005 0.100 4363 Dihedral : 13.748 167.050 9226 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1277 sheet: 0.82 (0.22), residues: 511 loop : 0.03 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 264 TYR 0.025 0.001 TYR G 175 PHE 0.011 0.001 PHE E 125 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (24684) covalent geometry : angle 0.60300 / 0.35 (33479) hydrogen bonds : bond 0.14982 / 10.33 ( 1157) hydrogen bonds : angle 6.16509 / 4.34 ( 3291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.825 Fit side-chains REVERT: B 418 GLU cc_start: 0.8319 (tp30) cc_final: 0.8068 (mp0) REVERT: D 56 ASP cc_start: 0.7984 (t0) cc_final: 0.7749 (t0) REVERT: D 311 ASP cc_start: 0.7999 (t70) cc_final: 0.7732 (t0) REVERT: D 469 MET cc_start: 0.8388 (mtm) cc_final: 0.8177 (mtp) REVERT: E 407 GLN cc_start: 0.8732 (tt0) cc_final: 0.8398 (tt0) REVERT: G 26 MET cc_start: 0.7575 (mmm) cc_final: 0.6866 (mmm) outliers start: 0 outliers final: 1 residues processed: 201 average time/residue: 0.5551 time to fit residues: 129.2629 Evaluate side-chains 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 70 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074264 restraints weight = 47576.883| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.48 r_work: 0.2908 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24684 Z= 0.247 Angle : 0.624 7.470 33479 Z= 0.329 Chirality : 0.049 0.189 3856 Planarity : 0.005 0.042 4363 Dihedral : 6.497 157.660 3427 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 1.21 % Allowed : 6.81 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3115 helix: 1.12 (0.15), residues: 1274 sheet: 0.53 (0.22), residues: 530 loop : -0.14 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 264 TYR 0.019 0.002 TYR G 91 PHE 0.028 0.002 PHE B 350 HIS 0.011 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (24684) covalent geometry : angle 0.62408 / 0.33 (33479) hydrogen bonds : bond 0.05216 / 3.52 ( 1157) hydrogen bonds : angle 5.23464 / 3.67 ( 3291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.935 Fit side-chains REVERT: B 418 GLU cc_start: 0.8788 (tp30) cc_final: 0.8472 (mp0) REVERT: C 67 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: D 56 ASP cc_start: 0.8560 (t0) cc_final: 0.8253 (t0) REVERT: D 285 MET cc_start: 0.9299 (tpt) cc_final: 0.9090 (tpp) REVERT: D 311 ASP cc_start: 0.8422 (t70) cc_final: 0.8047 (t0) REVERT: D 469 MET cc_start: 0.8602 (mtm) cc_final: 0.8337 (mtp) REVERT: E 392 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7917 (mm) REVERT: E 407 GLN cc_start: 0.8901 (tt0) cc_final: 0.8558 (tt0) REVERT: F 235 MET cc_start: 0.9075 (mtt) cc_final: 0.8862 (mtt) REVERT: G 26 MET cc_start: 0.7347 (mmm) cc_final: 0.6533 (mmm) REVERT: G 34 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.4605 (ttp80) outliers start: 31 outliers final: 11 residues processed: 171 average time/residue: 0.5822 time to fit residues: 115.6911 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 117 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076707 restraints weight = 46945.756| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.49 r_work: 0.2954 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24684 Z= 0.127 Angle : 0.525 7.756 33479 Z= 0.274 Chirality : 0.044 0.149 3856 Planarity : 0.004 0.042 4363 Dihedral : 5.921 147.150 3425 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.17 % Allowed : 9.00 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1278 sheet: 0.62 (0.22), residues: 530 loop : -0.05 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.014 0.001 TYR G 262 PHE 0.020 0.001 PHE B 350 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24684) covalent geometry : angle 0.52480 / 0.27 (33479) hydrogen bonds : bond 0.03982 / 2.68 ( 1157) hydrogen bonds : angle 4.86600 / 3.41 ( 3291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.817 Fit side-chains REVERT: A 189 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: B 418 GLU cc_start: 0.8768 (tp30) cc_final: 0.8436 (mp0) REVERT: D 56 ASP cc_start: 0.8613 (t0) cc_final: 0.8279 (t0) REVERT: D 311 ASP cc_start: 0.8395 (t70) cc_final: 0.7981 (t0) REVERT: D 469 MET cc_start: 0.8668 (mtm) cc_final: 0.8113 (mtm) REVERT: E 333 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8368 (tpp-160) REVERT: E 407 GLN cc_start: 0.8864 (tt0) cc_final: 0.8506 (tt0) REVERT: G 26 MET cc_start: 0.7279 (mmm) cc_final: 0.6499 (mmm) REVERT: G 44 PRO cc_start: 0.6453 (Cg_endo) cc_final: 0.6241 (Cg_exo) REVERT: G 175 TYR cc_start: 0.3699 (p90) cc_final: 0.3137 (p90) REVERT: G 270 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6828 (tp) outliers start: 30 outliers final: 10 residues processed: 184 average time/residue: 0.5298 time to fit residues: 114.1764 Evaluate side-chains 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 245 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN G 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074878 restraints weight = 47071.473| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.47 r_work: 0.2920 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24684 Z= 0.205 Angle : 0.583 9.225 33479 Z= 0.303 Chirality : 0.047 0.160 3856 Planarity : 0.005 0.043 4363 Dihedral : 6.019 147.289 3425 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 9.97 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3115 helix: 1.29 (0.15), residues: 1269 sheet: 0.54 (0.22), residues: 522 loop : -0.18 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 333 TYR 0.018 0.001 TYR G 91 PHE 0.036 0.002 PHE G 126 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.20 (24684) covalent geometry : angle 0.58338 / 0.30 (33479) hydrogen bonds : bond 0.04643 / 3.12 ( 1157) hydrogen bonds : angle 4.94422 / 3.46 ( 3291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.742 Fit side-chains REVERT: A 189 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 418 GLU cc_start: 0.8797 (tp30) cc_final: 0.8446 (mp0) REVERT: B 435 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8846 (mm) REVERT: C 499 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8836 (m) REVERT: D 56 ASP cc_start: 0.8647 (t0) cc_final: 0.8313 (t0) REVERT: D 311 ASP cc_start: 0.8423 (t70) cc_final: 0.7993 (t0) REVERT: D 469 MET cc_start: 0.8595 (mtm) cc_final: 0.8108 (mtm) REVERT: E 333 ARG cc_start: 0.8694 (tpp80) cc_final: 0.8340 (tpp-160) REVERT: E 389 MET cc_start: 0.7398 (tpt) cc_final: 0.7079 (tpp) REVERT: E 407 GLN cc_start: 0.8885 (tt0) cc_final: 0.8527 (tt0) REVERT: G 26 MET cc_start: 0.7283 (mmm) cc_final: 0.6488 (mmm) REVERT: G 167 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5871 (pp20) REVERT: G 175 TYR cc_start: 0.3752 (p90) cc_final: 0.3143 (p90) REVERT: G 191 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5921 (tm) REVERT: G 200 ARG cc_start: 0.2607 (mpt180) cc_final: 0.1777 (ppt170) REVERT: G 267 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: G 270 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6854 (tp) outliers start: 46 outliers final: 21 residues processed: 187 average time/residue: 0.5215 time to fit residues: 113.8868 Evaluate side-chains 167 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 267 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 301 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076941 restraints weight = 46588.149| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.47 r_work: 0.2956 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24684 Z= 0.120 Angle : 0.520 7.623 33479 Z= 0.268 Chirality : 0.044 0.147 3856 Planarity : 0.004 0.043 4363 Dihedral : 5.711 146.848 3425 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 1.56 % Allowed : 11.10 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3115 helix: 1.49 (0.15), residues: 1271 sheet: 0.64 (0.23), residues: 521 loop : -0.03 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 333 TYR 0.015 0.001 TYR G 91 PHE 0.015 0.001 PHE B 350 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (24684) covalent geometry : angle 0.51972 / 0.27 (33479) hydrogen bonds : bond 0.03728 / 2.51 ( 1157) hydrogen bonds : angle 4.71048 / 3.29 ( 3291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.674 Fit side-chains REVERT: A 189 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 191 MET cc_start: 0.8632 (ttp) cc_final: 0.8340 (ttp) REVERT: D 56 ASP cc_start: 0.8635 (t0) cc_final: 0.8273 (t0) REVERT: D 311 ASP cc_start: 0.8375 (t70) cc_final: 0.7885 (t0) REVERT: D 469 MET cc_start: 0.8522 (mtm) cc_final: 0.8287 (mtp) REVERT: E 2 THR cc_start: 0.6673 (OUTLIER) cc_final: 0.6096 (t) REVERT: E 333 ARG cc_start: 0.8668 (tpp80) cc_final: 0.8332 (tpp-160) REVERT: E 407 GLN cc_start: 0.8832 (tt0) cc_final: 0.8459 (tt0) REVERT: G 26 MET cc_start: 0.7265 (mmm) cc_final: 0.6456 (mmm) REVERT: G 143 GLN cc_start: 0.6096 (pp30) cc_final: 0.5827 (pp30) REVERT: G 175 TYR cc_start: 0.3794 (p90) cc_final: 0.3251 (p90) REVERT: G 200 ARG cc_start: 0.2591 (mpt180) cc_final: 0.1688 (ppt170) REVERT: G 270 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6763 (tp) outliers start: 40 outliers final: 20 residues processed: 185 average time/residue: 0.4973 time to fit residues: 108.3383 Evaluate side-chains 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 165 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 273 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074277 restraints weight = 47574.778| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.49 r_work: 0.2909 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24684 Z= 0.222 Angle : 0.595 10.224 33479 Z= 0.306 Chirality : 0.047 0.159 3856 Planarity : 0.005 0.042 4363 Dihedral : 5.984 160.278 3425 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.14 % Allowed : 11.29 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3115 helix: 1.32 (0.15), residues: 1268 sheet: 0.51 (0.23), residues: 518 loop : -0.19 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 333 TYR 0.020 0.001 TYR G 91 PHE 0.017 0.002 PHE G 126 HIS 0.008 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (24684) covalent geometry : angle 0.59512 / 0.31 (33479) hydrogen bonds : bond 0.04650 / 3.13 ( 1157) hydrogen bonds : angle 4.88372 / 3.41 ( 3291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.858 Fit side-chains REVERT: A 189 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: B 191 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: B 435 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8878 (mm) REVERT: C 499 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8859 (m) REVERT: D 56 ASP cc_start: 0.8651 (t0) cc_final: 0.8296 (t0) REVERT: D 311 ASP cc_start: 0.8479 (t70) cc_final: 0.7992 (t0) REVERT: D 469 MET cc_start: 0.8459 (mtm) cc_final: 0.8255 (mtp) REVERT: E 2 THR cc_start: 0.6619 (OUTLIER) cc_final: 0.6028 (t) REVERT: E 271 MET cc_start: 0.9073 (mtp) cc_final: 0.8765 (ttm) REVERT: E 333 ARG cc_start: 0.8679 (tpp80) cc_final: 0.8333 (tpp-160) REVERT: E 389 MET cc_start: 0.7498 (tpt) cc_final: 0.7200 (tpp) REVERT: E 407 GLN cc_start: 0.8875 (tt0) cc_final: 0.8510 (tt0) REVERT: G 26 MET cc_start: 0.7237 (mmm) cc_final: 0.6412 (mmm) REVERT: G 126 PHE cc_start: 0.6180 (m-80) cc_final: 0.5761 (m-80) REVERT: G 143 GLN cc_start: 0.5897 (pp30) cc_final: 0.5651 (pp30) REVERT: G 167 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5937 (pp20) REVERT: G 175 TYR cc_start: 0.3813 (p90) cc_final: 0.3235 (p90) REVERT: G 200 ARG cc_start: 0.2568 (mpt180) cc_final: 0.1701 (ppt170) REVERT: G 267 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: G 270 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6716 (tp) outliers start: 55 outliers final: 35 residues processed: 193 average time/residue: 0.4924 time to fit residues: 112.3594 Evaluate side-chains 184 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 296 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074677 restraints weight = 47288.528| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.47 r_work: 0.2914 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24684 Z= 0.192 Angle : 0.580 10.216 33479 Z= 0.297 Chirality : 0.046 0.155 3856 Planarity : 0.004 0.043 4363 Dihedral : 6.026 169.122 3425 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.22 % Allowed : 11.80 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1262 sheet: 0.51 (0.23), residues: 509 loop : -0.19 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.018 0.001 TYR G 91 PHE 0.015 0.001 PHE G 126 HIS 0.007 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (24684) covalent geometry : angle 0.58045 / 0.30 (33479) hydrogen bonds : bond 0.04446 / 2.99 ( 1157) hydrogen bonds : angle 4.84293 / 3.38 ( 3291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 0.665 Fit side-chains REVERT: B 191 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8347 (ttp) REVERT: B 435 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8860 (mm) REVERT: D 56 ASP cc_start: 0.8655 (t0) cc_final: 0.8263 (t0) REVERT: D 311 ASP cc_start: 0.8470 (t70) cc_final: 0.7974 (t0) REVERT: E 2 THR cc_start: 0.6625 (OUTLIER) cc_final: 0.6026 (t) REVERT: E 271 MET cc_start: 0.9077 (mtp) cc_final: 0.8773 (ttm) REVERT: E 333 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8339 (tpp-160) REVERT: E 407 GLN cc_start: 0.8865 (tt0) cc_final: 0.8543 (tt0) REVERT: G 26 MET cc_start: 0.7278 (mmm) cc_final: 0.6457 (mmm) REVERT: G 125 PHE cc_start: 0.6638 (t80) cc_final: 0.6350 (t80) REVERT: G 126 PHE cc_start: 0.6211 (m-80) cc_final: 0.5796 (m-80) REVERT: G 143 GLN cc_start: 0.5935 (pp30) cc_final: 0.5676 (pp30) REVERT: G 167 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5996 (pp20) REVERT: G 175 TYR cc_start: 0.3846 (p90) cc_final: 0.3237 (p90) REVERT: G 200 ARG cc_start: 0.2632 (mpt180) cc_final: 0.1686 (ppt170) REVERT: G 267 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6968 (pt0) REVERT: G 270 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6680 (tp) REVERT: G 273 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8396 (pp20) outliers start: 57 outliers final: 37 residues processed: 190 average time/residue: 0.4661 time to fit residues: 104.8158 Evaluate side-chains 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 70 optimal weight: 6.9990 chunk 273 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075007 restraints weight = 47220.273| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.48 r_work: 0.2920 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24684 Z= 0.174 Angle : 0.577 10.953 33479 Z= 0.293 Chirality : 0.046 0.167 3856 Planarity : 0.004 0.043 4363 Dihedral : 6.010 173.706 3425 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 12.38 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1260 sheet: 0.54 (0.23), residues: 501 loop : -0.15 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 3 TYR 0.017 0.001 TYR G 91 PHE 0.014 0.001 PHE E 125 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (24684) covalent geometry : angle 0.57672 / 0.29 (33479) hydrogen bonds : bond 0.04313 / 2.90 ( 1157) hydrogen bonds : angle 4.80011 / 3.35 ( 3291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.635 Fit side-chains REVERT: B 191 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8342 (ttp) REVERT: B 435 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8880 (mm) REVERT: D 56 ASP cc_start: 0.8626 (t0) cc_final: 0.8240 (t0) REVERT: D 311 ASP cc_start: 0.8471 (t70) cc_final: 0.7971 (t0) REVERT: D 469 MET cc_start: 0.8404 (mtp) cc_final: 0.8126 (mtm) REVERT: E 2 THR cc_start: 0.6631 (OUTLIER) cc_final: 0.6045 (t) REVERT: E 271 MET cc_start: 0.9075 (mtp) cc_final: 0.8773 (ttm) REVERT: E 333 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8352 (tpp-160) REVERT: E 389 MET cc_start: 0.7512 (tpt) cc_final: 0.7181 (tpp) REVERT: E 407 GLN cc_start: 0.8862 (tt0) cc_final: 0.8504 (tt0) REVERT: F 389 MET cc_start: 0.8457 (tpp) cc_final: 0.8168 (tpp) REVERT: G 26 MET cc_start: 0.7262 (mmm) cc_final: 0.6448 (mmm) REVERT: G 125 PHE cc_start: 0.6625 (t80) cc_final: 0.6337 (t80) REVERT: G 126 PHE cc_start: 0.6186 (m-80) cc_final: 0.5828 (m-80) REVERT: G 143 GLN cc_start: 0.5956 (pp30) cc_final: 0.5691 (pp30) REVERT: G 167 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.5994 (pp20) REVERT: G 175 TYR cc_start: 0.3848 (p90) cc_final: 0.3234 (p90) REVERT: G 200 ARG cc_start: 0.2519 (mpt180) cc_final: 0.1657 (ppt170) REVERT: G 267 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6992 (pt0) REVERT: G 270 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6621 (tp) REVERT: G 273 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8334 (pp20) outliers start: 54 outliers final: 39 residues processed: 187 average time/residue: 0.4666 time to fit residues: 103.1925 Evaluate side-chains 190 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 154 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 208 optimal weight: 0.0050 chunk 148 optimal weight: 8.9990 chunk 262 optimal weight: 0.3980 chunk 206 optimal weight: 0.3980 chunk 222 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078868 restraints weight = 46793.517| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.49 r_work: 0.2996 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24684 Z= 0.094 Angle : 0.517 11.748 33479 Z= 0.260 Chirality : 0.043 0.145 3856 Planarity : 0.004 0.043 4363 Dihedral : 5.587 176.110 3425 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 1.13 % Allowed : 13.47 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1267 sheet: 0.81 (0.23), residues: 488 loop : 0.07 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.011 0.001 TYR B 79 PHE 0.014 0.001 PHE G 146 HIS 0.004 0.000 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (24684) covalent geometry : angle 0.51728 / 0.26 (33479) hydrogen bonds : bond 0.03100 / 2.09 ( 1157) hydrogen bonds : angle 4.50320 / 3.14 ( 3291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.662 Fit side-chains REVERT: A 121 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 191 MET cc_start: 0.8520 (ttp) cc_final: 0.8245 (ttp) REVERT: B 435 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8826 (mm) REVERT: D 56 ASP cc_start: 0.8595 (t0) cc_final: 0.8228 (t0) REVERT: D 311 ASP cc_start: 0.8254 (t70) cc_final: 0.7769 (t0) REVERT: D 469 MET cc_start: 0.8391 (mtp) cc_final: 0.8111 (mtm) REVERT: E 2 THR cc_start: 0.6613 (OUTLIER) cc_final: 0.6033 (t) REVERT: E 389 MET cc_start: 0.7418 (tpt) cc_final: 0.7134 (tpp) REVERT: F 59 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8748 (p) REVERT: G 26 MET cc_start: 0.7261 (mmm) cc_final: 0.6503 (mmm) REVERT: G 125 PHE cc_start: 0.6517 (t80) cc_final: 0.6250 (t80) REVERT: G 126 PHE cc_start: 0.6175 (m-80) cc_final: 0.5796 (m-80) REVERT: G 143 GLN cc_start: 0.5911 (pp30) cc_final: 0.5629 (pp30) REVERT: G 167 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5868 (pp20) REVERT: G 175 TYR cc_start: 0.3876 (p90) cc_final: 0.3146 (p90) REVERT: G 270 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6852 (tp) REVERT: G 273 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8491 (pp20) outliers start: 29 outliers final: 12 residues processed: 193 average time/residue: 0.5072 time to fit residues: 114.8265 Evaluate side-chains 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 149 optimal weight: 0.9980 chunk 299 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 291 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078253 restraints weight = 46755.465| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.49 r_work: 0.2979 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24684 Z= 0.104 Angle : 0.534 15.215 33479 Z= 0.267 Chirality : 0.043 0.168 3856 Planarity : 0.004 0.042 4363 Dihedral : 5.533 176.080 3425 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Rotamer: Outliers : 0.97 % Allowed : 14.37 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1264 sheet: 0.86 (0.23), residues: 506 loop : 0.08 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 333 TYR 0.012 0.001 TYR B 79 PHE 0.012 0.001 PHE B 350 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (24684) covalent geometry : angle 0.53381 / 0.27 (33479) hydrogen bonds : bond 0.03319 / 2.23 ( 1157) hydrogen bonds : angle 4.49915 / 3.14 ( 3291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.598 Fit side-chains REVERT: A 121 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 191 MET cc_start: 0.8534 (ttp) cc_final: 0.8235 (ttp) REVERT: B 435 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 461 TYR cc_start: 0.8178 (m-10) cc_final: 0.7890 (m-10) REVERT: D 56 ASP cc_start: 0.8593 (t0) cc_final: 0.8240 (t0) REVERT: D 311 ASP cc_start: 0.8270 (t70) cc_final: 0.7801 (t0) REVERT: D 469 MET cc_start: 0.8383 (mtp) cc_final: 0.8091 (mtm) REVERT: E 2 THR cc_start: 0.6610 (OUTLIER) cc_final: 0.6023 (t) REVERT: E 271 MET cc_start: 0.8895 (mtp) cc_final: 0.8658 (ttt) REVERT: E 333 ARG cc_start: 0.8650 (tpp80) cc_final: 0.8222 (tpp-160) REVERT: E 389 MET cc_start: 0.7462 (tpt) cc_final: 0.7164 (tpp) REVERT: F 59 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (p) REVERT: G 26 MET cc_start: 0.7234 (mmm) cc_final: 0.6464 (mmm) REVERT: G 125 PHE cc_start: 0.6536 (t80) cc_final: 0.6227 (t80) REVERT: G 126 PHE cc_start: 0.6059 (m-80) cc_final: 0.5747 (m-80) REVERT: G 143 GLN cc_start: 0.5855 (pp30) cc_final: 0.5581 (pp30) REVERT: G 167 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5940 (pp20) REVERT: G 175 TYR cc_start: 0.3880 (p90) cc_final: 0.3167 (p90) REVERT: G 273 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8461 (pp20) outliers start: 25 outliers final: 16 residues processed: 174 average time/residue: 0.5038 time to fit residues: 103.1378 Evaluate side-chains 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 298 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 191 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 132 optimal weight: 0.0050 chunk 222 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076008 restraints weight = 46934.250| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.48 r_work: 0.2939 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24684 Z= 0.175 Angle : 0.581 15.120 33479 Z= 0.293 Chirality : 0.046 0.174 3856 Planarity : 0.004 0.042 4363 Dihedral : 5.782 179.214 3425 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.13 % Allowed : 14.21 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1267 sheet: 0.73 (0.23), residues: 509 loop : -0.04 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 333 TYR 0.016 0.001 TYR G 91 PHE 0.014 0.001 PHE E 125 HIS 0.006 0.001 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (24684) covalent geometry : angle 0.58083 / 0.29 (33479) hydrogen bonds : bond 0.04029 / 2.71 ( 1157) hydrogen bonds : angle 4.64758 / 3.24 ( 3291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.93 seconds wall clock time: 101 minutes 20.38 seconds (6080.38 seconds total)