Starting phenix.real_space_refine on Fri Feb 6 09:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839.map" model { file = "/net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvl_49839/02_2026/9nvl_49839_neut.cif" } resolution = 2.46 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= 0.048 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 8 5.49 5 Mg 3 5.21 5 S 88 5.16 5 C 15270 2.51 5 N 4185 2.21 5 O 4636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24190 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3640 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3651 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3633 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 22, 'TRANS': 450} Chain: "D" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3660 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} Chain: "E" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3651 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 27, 'TRANS': 440} Chain: "F" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3651 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 24190 At special positions: 0 Unit cell: (153.72, 124.32, 126.84, 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 88 16.00 P 8 15.00 Mg 3 11.99 O 4636 8.00 N 4185 7.00 C 15270 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: 1.73 Conformation dependent library (CDL) restraints added in 869.1 milliseconds 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 20 sheets defined 48.2% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.233A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.696A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.804A pdb=" N ALA A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.651A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.660A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.692A pdb=" N HIS A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) 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: 3.647A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 396 removed outlier: 4.102A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 4.165A pdb=" N GLN A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 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 removed outlier: 4.192A pdb=" N LEU A 472 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.533A pdb=" N LYS A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.392A pdb=" N GLY B 81 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.678A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.557A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.534A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.655A pdb=" N HIS B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) 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: 3.780A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 removed outlier: 3.675A pdb=" N TYR B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.776A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 4.270A pdb=" N ARG B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 4.004A pdb=" N GLN B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 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 Processing helix chain 'B' and resid 468 through 479 removed outlier: 4.173A pdb=" N LEU B 472 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.889A pdb=" N LYS B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.300A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.716A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.512A pdb=" N ALA C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.678A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 4.101A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.848A pdb=" N HIS C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.670A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.508A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.534A pdb=" N TYR C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 394 removed outlier: 3.670A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (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 452 through 467 removed outlier: 3.673A pdb=" N ASP C 458 " --> pdb=" O LYS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 484 through 496 removed outlier: 3.532A pdb=" N ILE C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 162 through 177 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.598A pdb=" N ASN D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 241 removed outlier: 5.224A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 268 removed outlier: 3.856A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 279 through 289 removed outlier: 3.927A pdb=" N LEU D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 314 through 321 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 379 through 386 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 392 through 409 removed outlier: 3.731A pdb=" N ARG D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.651A pdb=" N THR D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 441 Processing helix chain 'D' and resid 448 through 453 removed outlier: 3.535A pdb=" N TYR D 453 " --> pdb=" O GLN D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.640A pdb=" N ALA D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 466 " --> pdb=" O VAL D 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.757A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 92 " --> pdb=" O PRO E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 92' Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.566A pdb=" N GLN E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 162 through 177 Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.707A pdb=" N ASP E 208 " --> pdb=" O GLY E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 220 through 241 removed outlier: 3.527A pdb=" N ARG E 224 " --> pdb=" O PRO E 220 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU E 229 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 231 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 268 Processing helix chain 'E' and resid 272 through 276 removed outlier: 3.569A pdb=" N TYR E 276 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 289 removed outlier: 4.033A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 314 through 321 Processing helix chain 'E' and resid 331 through 337 Processing helix chain 'E' and resid 359 through 378 Processing helix chain 'E' and resid 379 through 386 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.638A pdb=" N LEU E 391 " --> pdb=" O MET E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 409 removed outlier: 4.083A pdb=" N ARG E 407 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 428 through 441 Processing helix chain 'E' and resid 448 through 453 removed outlier: 3.538A pdb=" N TYR E 453 " --> pdb=" O GLN E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 468 removed outlier: 3.782A pdb=" N ALA E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.604A pdb=" N GLN F 127 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 241 removed outlier: 5.286A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU F 229 " --> pdb=" O PHE F 225 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 4.082A pdb=" N ALA F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 279 through 289 removed outlier: 3.554A pdb=" N LEU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 311 Processing helix chain 'F' and resid 314 through 321 removed outlier: 3.522A pdb=" N PHE F 321 " --> pdb=" O PRO F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 331 through 336 Processing helix chain 'F' and resid 359 through 378 Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 392 through 409 removed outlier: 3.639A pdb=" N ARG F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 428 through 441 Processing helix chain 'F' and resid 448 through 453 removed outlier: 3.609A pdb=" N TYR F 453 " --> pdb=" O GLN F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 467 Processing helix chain 'G' and resid 7 through 62 removed outlier: 3.545A pdb=" N ARG G 37 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 93 through 108 removed outlier: 4.057A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.983A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 286 removed outlier: 4.006A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.639A pdb=" N GLN G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.540A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.692A 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 109 removed outlier: 6.544A pdb=" N VAL A 108 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR A 227 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ILE A 222 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A 224 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.351A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA F 29 " --> pdb=" O THR F 79 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN F 28 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.576A 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: 3.970A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.155A pdb=" N ARG B 106 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ILE B 222 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 256 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU B 316 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR B 260 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 170 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.429A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.899A 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: 8.285A pdb=" N ILE C 222 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU C 316 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR C 260 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.502A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.670A 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 87 removed outlier: 4.556A pdb=" N LYS D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.464A pdb=" N VAL D 183 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.626A pdb=" N ILE D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 10 removed outlier: 6.634A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.473A pdb=" N LYS E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 94 through 96 removed outlier: 6.100A pdb=" N ARG E 94 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE E 214 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE E 96 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLN E 216 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS E 152 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE E 328 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY E 154 " --> pdb=" O ILE E 328 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.469A pdb=" N LYS F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.379A pdb=" N ILE F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 210 through 212 removed outlier: 7.114A pdb=" N PHE F 181 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N PHE F 249 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL F 183 " --> pdb=" O PHE F 249 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL F 246 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL F 302 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU F 248 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA F 304 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE F 250 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR F 306 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE F 153 " --> pdb=" O GLN F 303 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE F 305 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU F 155 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.946A pdb=" N LEU G 138 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G 140 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR G 174 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU G 82 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ASN G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ILE G 84 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU G 185 " --> pdb=" O HIS G 177 " (cutoff:3.500A) 1122 hydrogen bonds defined for protein. 3192 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: 3.98 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5012 1.32 - 1.45: 4983 1.45 - 1.58: 14418 1.58 - 1.70: 8 1.70 - 1.83: 168 Bond restraints: 24589 Sorted by residual: bond pdb=" C4 ADP F 500 " pdb=" C5 ADP F 500 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C4 ADP D 500 " pdb=" C5 ADP D 500 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O1 PO4 C 603 " pdb=" P PO4 C 603 " ideal model delta sigma weight residual 1.565 1.448 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" O3 PO4 C 603 " pdb=" P PO4 C 603 " ideal model delta sigma weight residual 1.569 1.459 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" O2 PO4 C 603 " pdb=" P PO4 C 603 " ideal model delta sigma weight residual 1.567 1.460 0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 24584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.43: 32792 5.43 - 10.86: 462 10.86 - 16.28: 7 16.28 - 21.71: 2 21.71 - 27.14: 1 Bond angle restraints: 33264 Sorted by residual: angle pdb=" O ASP C 483 " pdb=" C ASP C 483 " pdb=" N GLU C 484 " ideal model delta sigma weight residual 122.59 95.45 27.14 1.33e+00 5.65e-01 4.16e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 123.15 13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" N VAL E 227 " pdb=" CA VAL E 227 " pdb=" C VAL E 227 " ideal model delta sigma weight residual 110.62 117.91 -7.29 1.02e+00 9.61e-01 5.11e+01 angle pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" C ARG C 354 " ideal model delta sigma weight residual 112.35 121.90 -9.55 1.34e+00 5.57e-01 5.08e+01 ... (remaining 33259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.08: 14413 23.08 - 46.16: 572 46.16 - 69.25: 88 69.25 - 92.33: 41 92.33 - 115.41: 3 Dihedral angle restraints: 15117 sinusoidal: 6228 harmonic: 8889 Sorted by residual: dihedral pdb=" C ARG C 354 " pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" CB ARG C 354 " ideal model delta harmonic sigma weight residual -122.60 -141.60 19.00 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" N ARG C 354 " pdb=" C ARG C 354 " pdb=" CA ARG C 354 " pdb=" CB ARG C 354 " ideal model delta harmonic sigma weight residual 122.80 139.62 -16.82 0 2.50e+00 1.60e-01 4.53e+01 dihedral pdb=" C ASN D 252 " pdb=" N ASN D 252 " pdb=" CA ASN D 252 " pdb=" CB ASN D 252 " ideal model delta harmonic sigma weight residual -122.60 -137.64 15.04 0 2.50e+00 1.60e-01 3.62e+01 ... (remaining 15114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 3311 0.163 - 0.326: 435 0.326 - 0.489: 30 0.489 - 0.652: 4 0.652 - 0.815: 1 Chirality restraints: 3781 Sorted by residual: chirality pdb=" CA ARG C 354 " pdb=" N ARG C 354 " pdb=" C ARG C 354 " pdb=" CB ARG C 354 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" CA ASN D 252 " pdb=" N ASN D 252 " pdb=" C ASN D 252 " pdb=" CB ASN D 252 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ARG C 278 " pdb=" N ARG C 278 " pdb=" C ARG C 278 " pdb=" CB ARG C 278 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 3778 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 483 " 0.081 2.00e-02 2.50e+03 1.33e-01 1.77e+02 pdb=" C ASP C 483 " -0.230 2.00e-02 2.50e+03 pdb=" O ASP C 483 " 0.076 2.00e-02 2.50e+03 pdb=" N GLU C 484 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP F 500 " -0.151 2.00e-02 2.50e+03 7.02e-02 1.36e+02 pdb=" C2 ADP F 500 " 0.064 2.00e-02 2.50e+03 pdb=" C4 ADP F 500 " 0.008 2.00e-02 2.50e+03 pdb=" C5 ADP F 500 " -0.022 2.00e-02 2.50e+03 pdb=" C6 ADP F 500 " -0.039 2.00e-02 2.50e+03 pdb=" C8 ADP F 500 " 0.124 2.00e-02 2.50e+03 pdb=" N1 ADP F 500 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP F 500 " 0.051 2.00e-02 2.50e+03 pdb=" N6 ADP F 500 " -0.078 2.00e-02 2.50e+03 pdb=" N7 ADP F 500 " 0.027 2.00e-02 2.50e+03 pdb=" N9 ADP F 500 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 389 " 0.118 2.00e-02 2.50e+03 6.22e-02 7.74e+01 pdb=" CG TYR B 389 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 389 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR B 389 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR B 389 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 389 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 389 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 389 " 0.087 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 12 2.44 - 3.06: 13518 3.06 - 3.67: 34785 3.67 - 4.29: 53111 4.29 - 4.90: 89275 Nonbonded interactions: 190701 Sorted by model distance: nonbonded pdb=" O2B ADP F 500 " pdb="MG MG F 501 " model vdw 1.828 2.170 nonbonded pdb=" O2A ADP F 500 " pdb="MG MG F 501 " model vdw 1.913 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 1.923 2.170 nonbonded pdb=" O1 PO4 C 603 " pdb="MG MG C 604 " model vdw 1.926 2.170 nonbonded pdb=" O3 PO4 C 603 " pdb="MG MG C 604 " model vdw 1.927 2.170 ... (remaining 190696 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 26 through 498) selection = (chain 'B' and resid 26 through 498) selection = (chain 'C' and resid 26 through 498) } ncs_group { reference = (chain 'D' and resid 2 through 469) selection = chain 'E' selection = (chain 'F' and resid 2 through 469) } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.510 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.013 0.143 24589 Z= 0.823 Angle : 2.026 27.140 33264 Z= 1.352 Chirality : 0.111 0.815 3781 Planarity : 0.015 0.183 4350 Dihedral : 13.374 115.408 9427 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.82 % Allowed : 5.25 % Favored : 93.93 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 3.18 % 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: -1.07 (0.14), residues: 3095 helix: -1.18 (0.12), residues: 1243 sheet: 0.74 (0.23), residues: 466 loop : -0.60 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 5 TYR 0.118 0.018 TYR B 389 PHE 0.074 0.012 PHE C 249 TRP 0.061 0.015 TRP E 198 HIS 0.018 0.004 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.01327 (24589) covalent geometry : angle 2.02557 (33264) hydrogen bonds : bond 0.21694 ( 1122) hydrogen bonds : angle 7.34440 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 571 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 391 GLU cc_start: 0.6498 (tt0) cc_final: 0.6273 (mm-30) REVERT: C 454 LYS cc_start: 0.7447 (tppt) cc_final: 0.7064 (mtpt) REVERT: D 10 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6653 (mtm) REVERT: D 201 MET cc_start: 0.6545 (mtm) cc_final: 0.5789 (mmt) REVERT: E 353 MET cc_start: 0.6635 (tpt) cc_final: 0.6377 (tpt) REVERT: E 468 MET cc_start: 0.0640 (mtm) cc_final: 0.0079 (mtm) REVERT: F 418 HIS cc_start: 0.5964 (m-70) cc_final: 0.5720 (m170) REVERT: G 34 LYS cc_start: 0.7195 (mttt) cc_final: 0.6987 (mttt) REVERT: G 244 MET cc_start: 0.6789 (ttp) cc_final: 0.6542 (ttp) outliers start: 21 outliers final: 5 residues processed: 585 average time/residue: 0.7359 time to fit residues: 482.1176 Evaluate side-chains 334 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 328 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 GLN ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 195 ASN D 216 GLN D 218 ASN D 362 HIS D 406 GLN D 414 HIS D 418 HIS E 195 ASN E 209 ASN E 252 ASN E 288 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS F 195 ASN F 362 HIS G 41 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.192668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.148833 restraints weight = 25774.076| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.40 r_work: 0.3756 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24589 Z= 0.171 Angle : 0.686 9.501 33264 Z= 0.366 Chirality : 0.049 0.250 3781 Planarity : 0.005 0.046 4350 Dihedral : 6.308 122.314 3454 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.97 % Allowed : 13.31 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.50 (0.15), residues: 3095 helix: 0.77 (0.14), residues: 1251 sheet: 0.85 (0.22), residues: 503 loop : -0.17 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 37 TYR 0.023 0.002 TYR G 265 PHE 0.024 0.002 PHE D 419 TRP 0.007 0.001 TRP D 198 HIS 0.005 0.001 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00368 (24589) covalent geometry : angle 0.68623 (33264) hydrogen bonds : bond 0.05487 ( 1122) hydrogen bonds : angle 5.08435 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 354 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6515 (pmtt) REVERT: A 385 ASP cc_start: 0.7568 (m-30) cc_final: 0.7271 (m-30) REVERT: B 67 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: B 127 ARG cc_start: 0.5730 (mtp-110) cc_final: 0.5373 (mtt180) REVERT: B 341 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: C 101 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: C 124 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6343 (mtmm) REVERT: C 159 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 283 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7318 (tpt90) REVERT: C 388 GLN cc_start: 0.7077 (mt0) cc_final: 0.6436 (tp40) REVERT: C 454 LYS cc_start: 0.7328 (tppt) cc_final: 0.6539 (mttt) REVERT: D 5 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6428 (mmt90) REVERT: D 33 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6020 (mt0) REVERT: D 37 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6864 (mtm-85) REVERT: D 112 LYS cc_start: 0.7375 (mtmt) cc_final: 0.6992 (pmtt) REVERT: D 201 MET cc_start: 0.6982 (mtm) cc_final: 0.5862 (mmt) REVERT: D 295 ARG cc_start: 0.7133 (mtm110) cc_final: 0.5960 (mpt-90) REVERT: D 403 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7127 (ttp80) REVERT: D 449 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6076 (mt-10) REVERT: E 52 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7896 (pp) REVERT: E 200 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5392 (mm-30) REVERT: E 381 ASP cc_start: 0.6525 (OUTLIER) cc_final: 0.6002 (p0) REVERT: F 5 ARG cc_start: 0.6840 (mtm-85) cc_final: 0.6609 (mtt180) REVERT: F 10 MET cc_start: 0.7739 (mpp) cc_final: 0.7367 (mmm) REVERT: F 131 ASP cc_start: 0.7616 (p0) cc_final: 0.7383 (p0) REVERT: F 149 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7920 (mtpt) REVERT: F 241 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7101 (mp0) REVERT: F 244 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.6579 (tttm) REVERT: F 398 ILE cc_start: 0.7872 (mt) cc_final: 0.7642 (mp) REVERT: F 400 GLN cc_start: 0.7332 (mt0) cc_final: 0.7020 (mp10) REVERT: F 418 HIS cc_start: 0.6036 (m-70) cc_final: 0.5575 (m-70) REVERT: F 450 GLN cc_start: 0.6885 (mt0) cc_final: 0.6674 (tp40) REVERT: G 29 MET cc_start: 0.5712 (mmt) cc_final: 0.5503 (mmp) REVERT: G 229 TYR cc_start: 0.6819 (t80) cc_final: 0.6392 (t80) REVERT: G 276 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7617 (mp0) outliers start: 102 outliers final: 18 residues processed: 418 average time/residue: 0.8058 time to fit residues: 377.8921 Evaluate side-chains 319 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 268 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 138 optimal weight: 0.1980 chunk 150 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 266 HIS A 294 HIS A 442 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN C 266 HIS C 371 GLN D 418 HIS F 218 ASN G 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.187414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142368 restraints weight = 25894.761| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.18 r_work: 0.3685 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24589 Z= 0.185 Angle : 0.687 8.066 33264 Z= 0.361 Chirality : 0.049 0.216 3781 Planarity : 0.006 0.057 4350 Dihedral : 6.327 120.639 3447 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.28 % Allowed : 15.64 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.51 (0.15), residues: 3095 helix: 0.87 (0.14), residues: 1281 sheet: 0.76 (0.22), residues: 516 loop : -0.26 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 415 TYR 0.022 0.002 TYR C 292 PHE 0.036 0.002 PHE E 408 TRP 0.007 0.001 TRP E 115 HIS 0.007 0.001 HIS E 414 Details of bonding type rmsd covalent geometry : bond 0.00424 (24589) covalent geometry : angle 0.68651 (33264) hydrogen bonds : bond 0.05793 ( 1122) hydrogen bonds : angle 4.90986 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 320 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6418 (pmtt) REVERT: A 385 ASP cc_start: 0.7614 (m-30) cc_final: 0.7327 (m-30) REVERT: A 454 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6649 (tppt) REVERT: B 67 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: B 95 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7633 (ttt) REVERT: B 127 ARG cc_start: 0.5784 (mtp-110) cc_final: 0.5522 (mtt180) REVERT: B 132 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7757 (ptpt) REVERT: B 173 THR cc_start: 0.6643 (t) cc_final: 0.6323 (t) REVERT: C 101 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: C 159 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7917 (mt) REVERT: C 365 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7328 (mtt90) REVERT: C 388 GLN cc_start: 0.6966 (mt0) cc_final: 0.6524 (tp40) REVERT: C 409 GLN cc_start: 0.7066 (mp10) cc_final: 0.6862 (mp10) REVERT: C 454 LYS cc_start: 0.7447 (tppt) cc_final: 0.6657 (mttt) REVERT: D 5 ARG cc_start: 0.7489 (mtm110) cc_final: 0.6649 (mmt90) REVERT: D 33 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.5927 (mt0) REVERT: D 119 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6936 (mtp-110) REVERT: D 201 MET cc_start: 0.7038 (mtm) cc_final: 0.5749 (mmt) REVERT: D 295 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6338 (mtt90) REVERT: E 52 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7876 (pp) REVERT: E 258 GLN cc_start: 0.7588 (mm-40) cc_final: 0.6920 (tm-30) REVERT: F 5 ARG cc_start: 0.6916 (mtm-85) cc_final: 0.6684 (mtt180) REVERT: F 10 MET cc_start: 0.7643 (mpp) cc_final: 0.7406 (mmm) REVERT: F 131 ASP cc_start: 0.7735 (p0) cc_final: 0.7351 (p0) REVERT: F 133 ILE cc_start: 0.7452 (mt) cc_final: 0.7247 (tt) REVERT: F 149 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7630 (tptp) REVERT: F 244 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7163 (tttm) REVERT: F 263 VAL cc_start: 0.7760 (t) cc_final: 0.7467 (p) REVERT: F 333 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: F 383 ILE cc_start: 0.6915 (mt) cc_final: 0.6618 (pp) REVERT: F 400 GLN cc_start: 0.7403 (mt0) cc_final: 0.7095 (mp10) REVERT: F 418 HIS cc_start: 0.6277 (m-70) cc_final: 0.5660 (m-70) REVERT: G 29 MET cc_start: 0.5770 (mmt) cc_final: 0.5510 (mmp) REVERT: G 173 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.4375 (ptm) REVERT: G 188 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5955 (mm-30) REVERT: G 229 TYR cc_start: 0.6838 (t80) cc_final: 0.6403 (t80) REVERT: G 276 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7556 (mp0) outliers start: 110 outliers final: 28 residues processed: 397 average time/residue: 0.7848 time to fit residues: 350.1585 Evaluate side-chains 323 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 119 ARG Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 32 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 252 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 186 GLN A 207 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 294 HIS ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 371 GLN D 418 HIS E 34 HIS F 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.186411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140588 restraints weight = 25913.579| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.08 r_work: 0.3674 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24589 Z= 0.173 Angle : 0.653 10.975 33264 Z= 0.341 Chirality : 0.047 0.231 3781 Planarity : 0.005 0.059 4350 Dihedral : 6.237 117.156 3447 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.12 % Allowed : 17.67 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.54 (0.15), residues: 3095 helix: 1.05 (0.15), residues: 1270 sheet: 0.66 (0.22), residues: 534 loop : -0.37 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 250 TYR 0.020 0.002 TYR A 438 PHE 0.016 0.002 PHE F 256 TRP 0.006 0.001 TRP D 198 HIS 0.004 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00404 (24589) covalent geometry : angle 0.65341 (33264) hydrogen bonds : bond 0.05241 ( 1122) hydrogen bonds : angle 4.78673 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 295 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6273 (pmtt) REVERT: A 307 GLU cc_start: 0.7607 (mp0) cc_final: 0.7363 (mp0) REVERT: A 385 ASP cc_start: 0.7725 (m-30) cc_final: 0.7385 (m-30) REVERT: A 454 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6680 (tppt) REVERT: B 67 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: B 95 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7576 (ttt) REVERT: B 103 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7813 (mt) REVERT: B 132 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7745 (ptpt) REVERT: B 173 THR cc_start: 0.6794 (t) cc_final: 0.6545 (t) REVERT: B 392 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6754 (tp) REVERT: C 101 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 159 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8007 (mt) REVERT: C 345 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: C 388 GLN cc_start: 0.6982 (mt0) cc_final: 0.6437 (tp40) REVERT: C 454 LYS cc_start: 0.7536 (tppt) cc_final: 0.6752 (mttt) REVERT: D 5 ARG cc_start: 0.7450 (mtm110) cc_final: 0.6628 (mmt90) REVERT: D 33 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.6010 (mt0) REVERT: D 199 LEU cc_start: 0.6897 (mp) cc_final: 0.6203 (mp) REVERT: D 201 MET cc_start: 0.7032 (mtm) cc_final: 0.5707 (mmt) REVERT: D 295 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6406 (mtt90) REVERT: D 380 GLN cc_start: 0.6737 (pt0) cc_final: 0.6482 (mt0) REVERT: E 52 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7891 (pp) REVERT: E 168 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.4005 (ttt) REVERT: E 258 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7172 (tt0) REVERT: E 296 ARG cc_start: 0.6522 (tpt90) cc_final: 0.6172 (tpt170) REVERT: F 5 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6676 (mtt180) REVERT: F 10 MET cc_start: 0.7547 (mpp) cc_final: 0.7316 (mmm) REVERT: F 117 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6275 (pt) REVERT: F 131 ASP cc_start: 0.7615 (p0) cc_final: 0.7295 (p0) REVERT: F 133 ILE cc_start: 0.7477 (mt) cc_final: 0.7238 (tt) REVERT: F 149 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7613 (tptp) REVERT: F 196 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6825 (tp30) REVERT: F 234 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: F 244 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7057 (tttm) REVERT: F 263 VAL cc_start: 0.7790 (t) cc_final: 0.7552 (p) REVERT: F 333 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: F 383 ILE cc_start: 0.6966 (mt) cc_final: 0.6667 (pp) REVERT: F 400 GLN cc_start: 0.7418 (mt0) cc_final: 0.7110 (mp10) REVERT: G 29 MET cc_start: 0.5838 (mmt) cc_final: 0.5584 (mmp) REVERT: G 229 TYR cc_start: 0.6869 (t80) cc_final: 0.6413 (t80) REVERT: G 234 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7700 (m-30) outliers start: 106 outliers final: 38 residues processed: 367 average time/residue: 0.7337 time to fit residues: 303.6726 Evaluate side-chains 331 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 337 LYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 274 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN C 57 ASN C 200 GLN C 433 GLN D 418 HIS E 40 ASN E 252 ASN G 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.186420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140502 restraints weight = 25853.989| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.05 r_work: 0.3676 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24589 Z= 0.157 Angle : 0.622 7.999 33264 Z= 0.324 Chirality : 0.046 0.204 3781 Planarity : 0.005 0.059 4350 Dihedral : 6.131 115.253 3447 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.24 % Allowed : 18.72 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.63 (0.15), residues: 3095 helix: 1.12 (0.15), residues: 1276 sheet: 0.69 (0.22), residues: 535 loop : -0.33 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 250 TYR 0.024 0.002 TYR B 438 PHE 0.034 0.002 PHE E 408 TRP 0.006 0.001 TRP D 198 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00358 (24589) covalent geometry : angle 0.62230 (33264) hydrogen bonds : bond 0.04977 ( 1122) hydrogen bonds : angle 4.72195 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 287 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7270 (t0) cc_final: 0.6745 (t0) REVERT: A 454 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6707 (tppt) REVERT: B 67 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: B 95 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7548 (ttt) REVERT: B 132 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7755 (ptpt) REVERT: B 173 THR cc_start: 0.6863 (t) cc_final: 0.6615 (t) REVERT: B 361 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7134 (tt) REVERT: B 467 LYS cc_start: 0.6930 (ptpp) cc_final: 0.6631 (ptpp) REVERT: C 101 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: C 296 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: C 388 GLN cc_start: 0.7083 (mt0) cc_final: 0.6464 (tp40) REVERT: C 454 LYS cc_start: 0.7606 (tppt) cc_final: 0.6847 (mttt) REVERT: D 3 ARG cc_start: 0.6853 (ptp90) cc_final: 0.6094 (pmm150) REVERT: D 5 ARG cc_start: 0.7462 (mtm110) cc_final: 0.6660 (mmt90) REVERT: D 33 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.5996 (mt0) REVERT: D 199 LEU cc_start: 0.6887 (mp) cc_final: 0.6170 (mp) REVERT: D 201 MET cc_start: 0.6975 (mtm) cc_final: 0.5667 (mmt) REVERT: D 295 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6397 (mtt90) REVERT: D 375 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6689 (ttt90) REVERT: E 33 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: E 52 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7890 (pp) REVERT: E 168 MET cc_start: 0.4677 (OUTLIER) cc_final: 0.4044 (ttt) REVERT: E 258 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7188 (tt0) REVERT: E 353 MET cc_start: 0.7669 (tpt) cc_final: 0.7453 (tpt) REVERT: E 370 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6337 (ttm-80) REVERT: F 5 ARG cc_start: 0.6966 (mtm-85) cc_final: 0.6743 (mtp85) REVERT: F 101 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: F 117 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6130 (pt) REVERT: F 131 ASP cc_start: 0.7620 (p0) cc_final: 0.7269 (p0) REVERT: F 133 ILE cc_start: 0.7448 (mt) cc_final: 0.7229 (tt) REVERT: F 149 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7608 (tptp) REVERT: F 196 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: F 244 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7116 (tttm) REVERT: F 296 ARG cc_start: 0.6841 (mtm180) cc_final: 0.5894 (tpt90) REVERT: F 333 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6699 (tp30) REVERT: F 383 ILE cc_start: 0.6958 (mt) cc_final: 0.6664 (pp) REVERT: G 29 MET cc_start: 0.5760 (mmt) cc_final: 0.5509 (mmp) REVERT: G 85 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (t) REVERT: G 173 MET cc_start: 0.4807 (mpt) cc_final: 0.4558 (ptm) REVERT: G 229 TYR cc_start: 0.6910 (t80) cc_final: 0.6463 (t80) REVERT: G 234 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7672 (m-30) outliers start: 109 outliers final: 35 residues processed: 356 average time/residue: 0.7454 time to fit residues: 298.9814 Evaluate side-chains 325 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 403 ARG Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 337 LYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 234 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 252 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 110 optimal weight: 0.0040 overall best weight: 4.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 409 GLN D 418 HIS E 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.184265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139418 restraints weight = 25950.068| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.02 r_work: 0.3639 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24589 Z= 0.212 Angle : 0.706 12.450 33264 Z= 0.366 Chirality : 0.049 0.235 3781 Planarity : 0.006 0.064 4350 Dihedral : 6.449 115.187 3447 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.63 % Allowed : 19.03 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.39 (0.15), residues: 3095 helix: 0.91 (0.14), residues: 1273 sheet: 0.67 (0.22), residues: 525 loop : -0.48 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 37 TYR 0.020 0.002 TYR C 463 PHE 0.017 0.002 PHE F 256 TRP 0.007 0.002 TRP D 198 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00506 (24589) covalent geometry : angle 0.70585 (33264) hydrogen bonds : bond 0.05755 ( 1122) hydrogen bonds : angle 4.86257 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 283 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6774 (tppt) REVERT: A 488 LYS cc_start: 0.6833 (mttp) cc_final: 0.6567 (mttt) REVERT: B 67 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: B 95 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7560 (ttt) REVERT: B 132 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7783 (ptpt) REVERT: B 173 THR cc_start: 0.6961 (t) cc_final: 0.6743 (t) REVERT: B 361 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 101 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: C 296 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7140 (ptp-170) REVERT: C 345 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7226 (mt-10) REVERT: C 373 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6185 (tmtm) REVERT: C 388 GLN cc_start: 0.7231 (mt0) cc_final: 0.6450 (tp40) REVERT: C 398 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.3372 (p90) REVERT: C 454 LYS cc_start: 0.7674 (tppt) cc_final: 0.6907 (mttt) REVERT: D 3 ARG cc_start: 0.6922 (ptp90) cc_final: 0.6208 (pmm150) REVERT: D 5 ARG cc_start: 0.7534 (mtm110) cc_final: 0.6767 (mmt90) REVERT: D 33 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.6091 (mt0) REVERT: D 199 LEU cc_start: 0.6990 (mp) cc_final: 0.6243 (mp) REVERT: D 201 MET cc_start: 0.7018 (mtm) cc_final: 0.5608 (mmt) REVERT: D 247 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7294 (tt) REVERT: D 295 ARG cc_start: 0.7155 (mtm110) cc_final: 0.6334 (mtt90) REVERT: D 333 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7217 (tm-30) REVERT: D 375 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6670 (ttt90) REVERT: E 33 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.5840 (mp10) REVERT: E 52 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7910 (pp) REVERT: E 168 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.4133 (ttt) REVERT: E 258 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7227 (tt0) REVERT: E 353 MET cc_start: 0.7804 (tpt) cc_final: 0.7515 (tpt) REVERT: E 404 LYS cc_start: 0.5789 (mtmt) cc_final: 0.5569 (ttmt) REVERT: E 454 MET cc_start: 0.5567 (mmt) cc_final: 0.5146 (mpp) REVERT: F 5 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6862 (mtp85) REVERT: F 10 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: F 44 ILE cc_start: 0.5907 (tp) cc_final: 0.5643 (mm) REVERT: F 117 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.6270 (pt) REVERT: F 131 ASP cc_start: 0.7600 (p0) cc_final: 0.7282 (p0) REVERT: F 149 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7688 (tptp) REVERT: F 196 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: F 234 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6831 (mtt) REVERT: F 244 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7102 (tttm) REVERT: F 251 ASP cc_start: 0.5815 (t70) cc_final: 0.5463 (p0) REVERT: F 296 ARG cc_start: 0.6832 (mtm180) cc_final: 0.6031 (tpt-90) REVERT: F 333 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: G 29 MET cc_start: 0.5908 (mmt) cc_final: 0.5642 (mmp) REVERT: G 173 MET cc_start: 0.4818 (mpt) cc_final: 0.4404 (ptm) REVERT: G 229 TYR cc_start: 0.6918 (t80) cc_final: 0.6429 (t80) REVERT: G 234 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7664 (m-30) outliers start: 119 outliers final: 48 residues processed: 364 average time/residue: 0.7473 time to fit residues: 307.3297 Evaluate side-chains 350 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 278 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 333 GLU Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 274 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 120 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 0.1980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.188015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142419 restraints weight = 25767.830| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.03 r_work: 0.3701 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24589 Z= 0.117 Angle : 0.566 9.056 33264 Z= 0.295 Chirality : 0.044 0.174 3781 Planarity : 0.004 0.060 4350 Dihedral : 5.903 113.269 3447 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.92 % Allowed : 20.93 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.79 (0.15), residues: 3095 helix: 1.33 (0.15), residues: 1269 sheet: 0.77 (0.22), residues: 530 loop : -0.32 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.023 0.001 TYR B 438 PHE 0.039 0.001 PHE E 408 TRP 0.009 0.001 TRP F 198 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00255 (24589) covalent geometry : angle 0.56579 (33264) hydrogen bonds : bond 0.04184 ( 1122) hydrogen bonds : angle 4.59235 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 292 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7327 (t0) cc_final: 0.6942 (t0) REVERT: A 385 ASP cc_start: 0.7849 (m-30) cc_final: 0.7567 (m-30) REVERT: A 454 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6911 (tppp) REVERT: B 95 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7504 (ttt) REVERT: B 132 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7757 (ptpt) REVERT: B 173 THR cc_start: 0.6982 (t) cc_final: 0.6692 (t) REVERT: B 467 LYS cc_start: 0.6960 (ptpp) cc_final: 0.6566 (ptpp) REVERT: C 101 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: C 130 GLU cc_start: 0.6170 (pm20) cc_final: 0.5622 (tp30) REVERT: C 388 GLN cc_start: 0.6992 (mt0) cc_final: 0.6330 (tp40) REVERT: C 454 LYS cc_start: 0.7526 (tppt) cc_final: 0.6752 (mttt) REVERT: D 3 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6083 (pmm150) REVERT: D 5 ARG cc_start: 0.7327 (mtm110) cc_final: 0.6594 (mmt90) REVERT: D 193 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6691 (mt-10) REVERT: D 201 MET cc_start: 0.6959 (mtm) cc_final: 0.5684 (mmt) REVERT: D 295 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6413 (mtt90) REVERT: D 333 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7140 (tm-30) REVERT: E 168 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4182 (ttt) REVERT: E 258 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7128 (tt0) REVERT: E 353 MET cc_start: 0.7776 (tpt) cc_final: 0.7414 (tpt) REVERT: E 404 LYS cc_start: 0.5798 (mtmt) cc_final: 0.5574 (ttmt) REVERT: E 454 MET cc_start: 0.5697 (mmt) cc_final: 0.5335 (mpp) REVERT: F 5 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6778 (mtp85) REVERT: F 101 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: F 131 ASP cc_start: 0.7573 (p0) cc_final: 0.7241 (p0) REVERT: F 133 ILE cc_start: 0.7421 (mt) cc_final: 0.7113 (tt) REVERT: F 196 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: F 234 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6722 (mtt) REVERT: F 244 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7072 (tptm) REVERT: F 296 ARG cc_start: 0.6787 (mtm180) cc_final: 0.6021 (tpt-90) REVERT: F 333 GLU cc_start: 0.7166 (tp30) cc_final: 0.6681 (tp30) REVERT: F 383 ILE cc_start: 0.6943 (mt) cc_final: 0.6678 (pp) REVERT: G 29 MET cc_start: 0.5766 (mmt) cc_final: 0.5511 (mmp) REVERT: G 173 MET cc_start: 0.4895 (mpt) cc_final: 0.4478 (ptm) REVERT: G 174 TYR cc_start: 0.5732 (m-80) cc_final: 0.5420 (m-80) REVERT: G 229 TYR cc_start: 0.6936 (t80) cc_final: 0.6386 (t80) outliers start: 75 outliers final: 28 residues processed: 339 average time/residue: 0.7176 time to fit residues: 273.2835 Evaluate side-chains 311 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 59 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 228 optimal weight: 0.0060 chunk 94 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 433 GLN E 252 ASN G 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.186867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141517 restraints weight = 25801.056| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.08 r_work: 0.3683 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24589 Z= 0.132 Angle : 0.590 9.059 33264 Z= 0.305 Chirality : 0.045 0.176 3781 Planarity : 0.005 0.061 4350 Dihedral : 5.856 108.400 3447 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.23 % Allowed : 20.74 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.81 (0.15), residues: 3095 helix: 1.34 (0.15), residues: 1276 sheet: 0.80 (0.22), residues: 526 loop : -0.32 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.022 0.001 TYR G 265 PHE 0.018 0.001 PHE F 256 TRP 0.008 0.001 TRP D 198 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00298 (24589) covalent geometry : angle 0.58964 (33264) hydrogen bonds : bond 0.04439 ( 1122) hydrogen bonds : angle 4.56262 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 276 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7396 (t0) cc_final: 0.6997 (t0) REVERT: A 385 ASP cc_start: 0.7815 (m-30) cc_final: 0.7541 (m-30) REVERT: A 454 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6843 (tppt) REVERT: B 95 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7546 (ttt) REVERT: B 132 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7773 (ptpt) REVERT: B 173 THR cc_start: 0.7017 (t) cc_final: 0.6756 (t) REVERT: B 467 LYS cc_start: 0.6949 (ptpp) cc_final: 0.6537 (ptpp) REVERT: C 60 MET cc_start: 0.7521 (mmt) cc_final: 0.7283 (mmt) REVERT: C 101 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 130 GLU cc_start: 0.6176 (pm20) cc_final: 0.5602 (tp30) REVERT: C 388 GLN cc_start: 0.7094 (mt0) cc_final: 0.6353 (tp40) REVERT: C 398 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.3404 (p90) REVERT: C 454 LYS cc_start: 0.7496 (tppt) cc_final: 0.6715 (mttt) REVERT: D 3 ARG cc_start: 0.6772 (ptp90) cc_final: 0.6073 (pmm150) REVERT: D 5 ARG cc_start: 0.7367 (mtm110) cc_final: 0.6619 (mmt90) REVERT: D 33 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5904 (mt0) REVERT: D 193 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6731 (mt-10) REVERT: D 201 MET cc_start: 0.6954 (mtm) cc_final: 0.5659 (mmt) REVERT: D 295 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6308 (mtt90) REVERT: D 375 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6699 (ttt90) REVERT: E 52 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7940 (pp) REVERT: E 168 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.4211 (ttt) REVERT: E 258 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7168 (tt0) REVERT: E 353 MET cc_start: 0.7754 (tpt) cc_final: 0.7338 (tpt) REVERT: E 370 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6281 (ttm-80) REVERT: E 454 MET cc_start: 0.5669 (mmt) cc_final: 0.5307 (mpp) REVERT: F 5 ARG cc_start: 0.7022 (mtm-85) cc_final: 0.6812 (mtp85) REVERT: F 52 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8122 (pp) REVERT: F 131 ASP cc_start: 0.7631 (p0) cc_final: 0.7272 (p0) REVERT: F 133 ILE cc_start: 0.7456 (mt) cc_final: 0.7188 (tt) REVERT: F 196 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: F 234 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6803 (mtt) REVERT: F 244 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7077 (tptm) REVERT: F 296 ARG cc_start: 0.6761 (mtm180) cc_final: 0.6001 (tpt-90) REVERT: F 333 GLU cc_start: 0.7186 (tp30) cc_final: 0.6699 (tp30) REVERT: G 29 MET cc_start: 0.5686 (mmt) cc_final: 0.5427 (mmp) REVERT: G 173 MET cc_start: 0.4910 (mpt) cc_final: 0.4487 (ptm) REVERT: G 229 TYR cc_start: 0.6951 (t80) cc_final: 0.6542 (t80) REVERT: G 234 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7497 (m-30) outliers start: 83 outliers final: 38 residues processed: 337 average time/residue: 0.7041 time to fit residues: 267.1436 Evaluate side-chains 325 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 375 ARG Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain E residue 396 LYS Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 234 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 242 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 240 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 147 optimal weight: 0.0010 chunk 279 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 269 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN C 409 GLN E 252 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144646 restraints weight = 25856.892| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.02 r_work: 0.3731 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24589 Z= 0.103 Angle : 0.539 8.722 33264 Z= 0.279 Chirality : 0.043 0.173 3781 Planarity : 0.004 0.058 4350 Dihedral : 5.464 97.164 3447 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 22.02 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 1.02 (0.15), residues: 3095 helix: 1.52 (0.15), residues: 1277 sheet: 0.86 (0.22), residues: 535 loop : -0.20 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 250 TYR 0.023 0.001 TYR G 265 PHE 0.037 0.001 PHE E 408 TRP 0.009 0.001 TRP F 198 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00221 (24589) covalent geometry : angle 0.53865 (33264) hydrogen bonds : bond 0.03587 ( 1122) hydrogen bonds : angle 4.41041 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 286 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7329 (t0) cc_final: 0.6994 (t0) REVERT: A 210 LYS cc_start: 0.7295 (mmtm) cc_final: 0.6247 (ttpt) REVERT: A 385 ASP cc_start: 0.7825 (m-30) cc_final: 0.7551 (m-30) REVERT: A 454 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6846 (tppt) REVERT: B 95 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7516 (ttt) REVERT: B 132 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7771 (ptpt) REVERT: B 173 THR cc_start: 0.6982 (t) cc_final: 0.6675 (t) REVERT: B 467 LYS cc_start: 0.6957 (ptpp) cc_final: 0.6583 (ptpp) REVERT: C 101 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: C 130 GLU cc_start: 0.6158 (pm20) cc_final: 0.5574 (tp30) REVERT: C 388 GLN cc_start: 0.6943 (mt0) cc_final: 0.6245 (tp40) REVERT: C 409 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: C 415 ARG cc_start: 0.7640 (mpt180) cc_final: 0.7365 (mmt180) REVERT: C 454 LYS cc_start: 0.7388 (tppt) cc_final: 0.6580 (mttt) REVERT: D 3 ARG cc_start: 0.6718 (ptp90) cc_final: 0.6018 (pmm150) REVERT: D 5 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6514 (mmt90) REVERT: D 7 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7382 (pt) REVERT: D 193 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6641 (mt-10) REVERT: D 201 MET cc_start: 0.6952 (mtm) cc_final: 0.5640 (mmt) REVERT: D 295 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6390 (mtt90) REVERT: D 333 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7111 (tm-30) REVERT: E 168 MET cc_start: 0.4794 (OUTLIER) cc_final: 0.4282 (ttt) REVERT: E 258 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7082 (tt0) REVERT: E 353 MET cc_start: 0.7830 (tpt) cc_final: 0.7378 (tpt) REVERT: E 370 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6307 (ttm-80) REVERT: E 454 MET cc_start: 0.5710 (mmt) cc_final: 0.5343 (mpp) REVERT: F 5 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6766 (mtp85) REVERT: F 131 ASP cc_start: 0.7557 (p0) cc_final: 0.7220 (p0) REVERT: F 133 ILE cc_start: 0.7472 (mt) cc_final: 0.7206 (tt) REVERT: F 234 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6682 (mtt) REVERT: F 244 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7116 (tttm) REVERT: F 296 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6069 (tpt-90) REVERT: F 333 GLU cc_start: 0.7151 (tp30) cc_final: 0.6661 (tp30) REVERT: F 383 ILE cc_start: 0.6938 (mt) cc_final: 0.6674 (pp) REVERT: G 29 MET cc_start: 0.5600 (mmt) cc_final: 0.5369 (mmp) REVERT: G 145 ASP cc_start: 0.6467 (m-30) cc_final: 0.6116 (p0) REVERT: G 173 MET cc_start: 0.4984 (mpt) cc_final: 0.4591 (ptm) REVERT: G 234 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7486 (m-30) outliers start: 52 outliers final: 23 residues processed: 320 average time/residue: 0.7258 time to fit residues: 261.9840 Evaluate side-chains 298 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 234 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 208 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN B 70 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN C 409 GLN C 433 GLN E 252 ASN G 266 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.184709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138679 restraints weight = 25969.269| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.06 r_work: 0.3656 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24589 Z= 0.199 Angle : 0.688 10.077 33264 Z= 0.355 Chirality : 0.048 0.222 3781 Planarity : 0.006 0.070 4350 Dihedral : 6.100 104.348 3447 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.33 % Allowed : 21.98 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.63 (0.15), residues: 3095 helix: 1.15 (0.15), residues: 1276 sheet: 0.75 (0.22), residues: 526 loop : -0.38 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 89 TYR 0.022 0.002 TYR G 265 PHE 0.018 0.002 PHE F 256 TRP 0.007 0.002 TRP E 115 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00473 (24589) covalent geometry : angle 0.68761 (33264) hydrogen bonds : bond 0.05358 ( 1122) hydrogen bonds : angle 4.66768 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6190 Ramachandran restraints generated. 3095 Oldfield, 0 Emsley, 3095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 454 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6835 (tppt) REVERT: B 95 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7573 (ttt) REVERT: B 132 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7778 (ptpt) REVERT: B 156 MET cc_start: 0.7390 (mtt) cc_final: 0.7159 (mtt) REVERT: B 173 THR cc_start: 0.7003 (t) cc_final: 0.6761 (t) REVERT: B 467 LYS cc_start: 0.6962 (ptpp) cc_final: 0.6601 (ptpp) REVERT: C 101 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: C 388 GLN cc_start: 0.7205 (mt0) cc_final: 0.6460 (tp40) REVERT: C 398 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.3558 (p90) REVERT: C 409 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6030 (mp-120) REVERT: C 454 LYS cc_start: 0.7537 (tppt) cc_final: 0.6773 (mttt) REVERT: D 3 ARG cc_start: 0.6785 (ptp90) cc_final: 0.6084 (pmm150) REVERT: D 5 ARG cc_start: 0.7464 (mtm110) cc_final: 0.6697 (mmt90) REVERT: D 201 MET cc_start: 0.6947 (mtm) cc_final: 0.5592 (mmt) REVERT: D 295 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6308 (mtt90) REVERT: E 52 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7957 (pp) REVERT: E 168 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4136 (ttt) REVERT: E 258 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7230 (tt0) REVERT: E 353 MET cc_start: 0.7792 (tpt) cc_final: 0.7433 (tpt) REVERT: E 364 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6710 (tm-30) REVERT: E 454 MET cc_start: 0.5553 (mmt) cc_final: 0.5203 (mpp) REVERT: F 5 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6840 (mtp85) REVERT: F 131 ASP cc_start: 0.7666 (p0) cc_final: 0.7286 (p0) REVERT: F 133 ILE cc_start: 0.7484 (mt) cc_final: 0.7220 (tt) REVERT: F 296 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6087 (tpt-90) REVERT: F 333 GLU cc_start: 0.7204 (tp30) cc_final: 0.6720 (tp30) REVERT: G 29 MET cc_start: 0.5681 (mmt) cc_final: 0.5426 (mmp) REVERT: G 173 MET cc_start: 0.4904 (mpt) cc_final: 0.4442 (ptm) REVERT: G 234 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7471 (m-30) outliers start: 60 outliers final: 33 residues processed: 305 average time/residue: 0.7084 time to fit residues: 243.6814 Evaluate side-chains 300 residues out of total 2570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 234 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 86 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 264 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 433 GLN E 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.187277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141697 restraints weight = 25889.730| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.10 r_work: 0.3692 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24589 Z= 0.127 Angle : 0.593 10.075 33264 Z= 0.306 Chirality : 0.045 0.176 3781 Planarity : 0.005 0.060 4350 Dihedral : 5.796 103.537 3447 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.14 % Allowed : 22.57 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % 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: 0.83 (0.15), residues: 3095 helix: 1.38 (0.15), residues: 1272 sheet: 0.77 (0.22), residues: 528 loop : -0.30 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 89 TYR 0.024 0.001 TYR B 438 PHE 0.037 0.001 PHE E 408 TRP 0.011 0.001 TRP F 198 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00287 (24589) covalent geometry : angle 0.59307 (33264) hydrogen bonds : bond 0.04246 ( 1122) hydrogen bonds : angle 4.53020 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10698.52 seconds wall clock time: 182 minutes 6.22 seconds (10926.22 seconds total)