Starting phenix.real_space_refine on Sat Jul 4 22:52:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9l_34572/07_2026/8h9l_34572.map" } resolution = 2.61 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= 0.028 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 13 5.49 5 Mg 5 5.21 5 S 85 5.16 5 C 15081 2.51 5 N 4170 2.21 5 O 4609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23963 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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} Chain: "D" 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: 5.01, per 1000 atoms: 0.21 Number of scatterers: 23963 At special positions: 0 Unit cell: (125.56, 123.37, 134.32, 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 85 16.00 P 13 15.00 Mg 5 11.99 O 4609 8.00 N 4170 7.00 C 15081 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5678 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 51.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.646A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.802A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.566A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.725A pdb=" N LYS A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.995A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.619A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.780A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.946A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.646A pdb=" N LYS A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 507 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.615A 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 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 4.058A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.602A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.833A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.522A pdb=" N GLY B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.545A pdb=" N GLN B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.627A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.639A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.520A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 removed outlier: 3.657A pdb=" N GLY B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.573A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.740A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 4.020A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.540A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 4.057A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.576A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.737A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.594A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.592A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 476 removed outlier: 4.398A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.611A pdb=" N MET E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.976A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.538A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 345 removed outlier: 3.531A pdb=" N LEU E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 391 removed outlier: 4.167A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.796A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 449 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.515A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.656A pdb=" N ALA E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.601A pdb=" N MET F 129 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 176 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.897A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 removed outlier: 4.178A pdb=" N PHE F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 345 removed outlier: 3.507A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 367 through 395 removed outlier: 4.843A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 removed outlier: 3.589A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.741A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 428 removed outlier: 3.826A pdb=" N GLU F 425 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL F 426 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 477 removed outlier: 3.517A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.957A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.165A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.772A pdb=" N GLY D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.013A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.673A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 465 through 480 removed outlier: 3.570A pdb=" N ALA D 469 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 224 through 271 Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 43 removed outlier: 3.721A pdb=" N GLU J 26 " --> pdb=" O PHE J 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 30 removed outlier: 3.735A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 139 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'O' and resid 156 through 159 Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.540A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 35 removed outlier: 6.561A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 5.665A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.727A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.666A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.710A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 6.618A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 6.675A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'O' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 150 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.073A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.311A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.134A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.667A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.248A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.403A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.243A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.161A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.228A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.186A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.461A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.154A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.202A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.314A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.162A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3231 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: 4.71 Time building geometry restraints manager: 2.40 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: 4574 1.32 - 1.44: 5299 1.44 - 1.56: 14250 1.56 - 1.69: 21 1.69 - 1.81: 163 Bond restraints: 24307 Sorted by residual: bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.453 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.282 0.092 1.00e-02 1.00e+04 8.51e+01 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.283 0.091 1.00e-02 1.00e+04 8.34e+01 ... (remaining 24302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 32600 3.41 - 6.81: 236 6.81 - 10.22: 31 10.22 - 13.63: 8 13.63 - 17.03: 3 Bond angle restraints: 32878 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.84 17.03 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.77 14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 124.91 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " pdb=" C8 ATP B 601 " ideal model delta sigma weight residual 105.72 115.08 -9.36 1.00e+00 1.00e+00 8.77e+01 ... (remaining 32873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.36: 14329 29.36 - 58.71: 437 58.71 - 88.07: 53 88.07 - 117.43: 5 117.43 - 146.78: 2 Dihedral angle restraints: 14826 sinusoidal: 5942 harmonic: 8884 Sorted by residual: dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.78 -146.78 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 171.03 128.97 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 48.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 14823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2486 0.049 - 0.099: 1078 0.099 - 0.148: 248 0.148 - 0.197: 11 0.197 - 0.247: 4 Chirality restraints: 3827 Sorted by residual: chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE C 121 " pdb=" N ILE C 121 " pdb=" C ILE C 121 " pdb=" CB ILE C 121 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 3824 not shown) Planarity restraints: 4250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.712 9.50e-02 1.11e+02 3.19e-01 6.21e+01 pdb=" NE ARG J 16 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" C ASN D 174 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 279 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C PRO D 279 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO D 279 " 0.014 2.00e-02 2.50e+03 pdb=" N SER D 280 " 0.012 2.00e-02 2.50e+03 ... (remaining 4247 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 73 2.41 - 3.03: 14523 3.03 - 3.65: 35589 3.65 - 4.28: 59991 4.28 - 4.90: 97409 Nonbonded interactions: 207585 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 1.782 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 1.890 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.975 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 2.052 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.082 2.170 ... (remaining 207580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } 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: 12.170 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.030 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:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 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 : 0.011 0.144 24307 Z= 0.526 Angle : 0.874 17.033 32878 Z= 0.538 Chirality : 0.054 0.247 3827 Planarity : 0.007 0.319 4250 Dihedral : 14.299 146.783 9148 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -2.29 (0.13), residues: 3102 helix: -1.50 (0.12), residues: 1333 sheet: -1.23 (0.22), residues: 479 loop : -1.46 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 277 TYR 0.015 0.002 TYR A 452 PHE 0.025 0.002 PHE J 34 HIS 0.005 0.001 HIS F 201 Details of bonding type rmsd/Z covalent geometry : bond 0.01091 / 0.53 (24307) covalent geometry : angle 0.87373 / 0.54 (32878) hydrogen bonds : bond 0.14764 / 10.12 ( 1135) hydrogen bonds : angle 6.91264 / 4.75 ( 3231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.882 Fit side-chains REVERT: B 498 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7529 (tptt) REVERT: C 124 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7702 (mttm) REVERT: C 386 VAL cc_start: 0.8129 (m) cc_final: 0.7800 (p) REVERT: C 457 GLU cc_start: 0.7607 (tt0) cc_final: 0.7312 (mt-10) REVERT: C 471 HIS cc_start: 0.6210 (t70) cc_final: 0.5502 (t-170) REVERT: D 390 ILE cc_start: 0.8420 (mt) cc_final: 0.8212 (mm) REVERT: D 475 LYS cc_start: 0.7664 (ttpt) cc_final: 0.7425 (tmtt) REVERT: O 107 THR cc_start: 0.8274 (t) cc_final: 0.8026 (p) REVERT: O 111 VAL cc_start: 0.7598 (p) cc_final: 0.7271 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.7492 time to fit residues: 323.6515 Evaluate side-chains 289 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 HIS A 385 GLN A 396 GLN A 475 GLN A 477 GLN A 503 ASN B 48 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN C 215 GLN C 385 GLN E 370 HIS F 27 GLN F 174 ASN F 180 HIS F 197 ASN F 296 GLN F 331 HIS F 458 GLN D 180 HIS D 266 GLN O 87 ASN O 92 ASN O 97 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100696 restraints weight = 31567.521| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.72 r_work: 0.3090 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24307 Z= 0.118 Angle : 0.521 10.330 32878 Z= 0.269 Chirality : 0.043 0.151 3827 Planarity : 0.004 0.041 4250 Dihedral : 6.496 136.418 3413 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.16 % Rotamer: Outliers : 1.34 % Allowed : 10.36 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -0.35 (0.15), residues: 3102 helix: 0.53 (0.14), residues: 1326 sheet: -0.73 (0.22), residues: 489 loop : -0.71 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 15 TYR 0.012 0.001 TYR C 397 PHE 0.016 0.001 PHE C 468 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (24307) covalent geometry : angle 0.52072 / 0.27 (32878) hydrogen bonds : bond 0.04310 / 2.99 ( 1135) hydrogen bonds : angle 5.05500 / 3.49 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 353 time to evaluate : 0.940 Fit side-chains REVERT: A 52 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8604 (mmm) REVERT: A 477 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7944 (mm110) REVERT: B 67 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: B 353 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8081 (mm-30) REVERT: B 373 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7954 (mmt90) REVERT: B 466 ASN cc_start: 0.8078 (m-40) cc_final: 0.7862 (m110) REVERT: B 498 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7092 (tptt) REVERT: C 124 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7502 (mttm) REVERT: C 471 HIS cc_start: 0.5872 (t70) cc_final: 0.5140 (t-170) REVERT: F 112 LYS cc_start: 0.8325 (mttt) cc_final: 0.7987 (mttp) REVERT: F 205 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7526 (mp0) REVERT: F 210 ASN cc_start: 0.8772 (t0) cc_final: 0.8394 (t0) REVERT: F 397 ASP cc_start: 0.7485 (m-30) cc_final: 0.7108 (m-30) REVERT: F 400 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7492 (p) REVERT: D 249 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: D 390 ILE cc_start: 0.8049 (mt) cc_final: 0.7817 (mm) REVERT: D 431 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7249 (tpt) REVERT: D 475 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7083 (tmtt) REVERT: G 233 ASP cc_start: 0.7840 (t70) cc_final: 0.7631 (t70) REVERT: O 136 THR cc_start: 0.7345 (m) cc_final: 0.7103 (p) outliers start: 34 outliers final: 10 residues processed: 369 average time/residue: 0.6915 time to fit residues: 288.3711 Evaluate side-chains 309 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 294 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 431 MET Chi-restraints excluded: chain D residue 434 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 7.9990 chunk 290 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN F 27 GLN F 458 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096840 restraints weight = 31682.713| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.72 r_work: 0.3054 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24307 Z= 0.174 Angle : 0.543 10.734 32878 Z= 0.278 Chirality : 0.044 0.139 3827 Planarity : 0.004 0.043 4250 Dihedral : 6.488 139.528 3413 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.03 % Rotamer: Outliers : 1.89 % Allowed : 12.37 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.19 (0.15), residues: 3102 helix: 1.04 (0.14), residues: 1331 sheet: -0.58 (0.23), residues: 486 loop : -0.45 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.011 0.001 TYR O 170 PHE 0.019 0.001 PHE J 34 HIS 0.006 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (24307) covalent geometry : angle 0.54297 / 0.28 (32878) hydrogen bonds : bond 0.04697 / 3.25 ( 1135) hydrogen bonds : angle 4.91931 / 3.39 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 0.820 Fit side-chains REVERT: A 355 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7936 (tt0) REVERT: B 67 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: B 353 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8063 (mm-30) REVERT: B 475 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: B 498 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7144 (tptt) REVERT: C 124 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7513 (mttm) REVERT: C 224 ASP cc_start: 0.8274 (t0) cc_final: 0.7660 (t0) REVERT: C 471 HIS cc_start: 0.5769 (t70) cc_final: 0.5061 (t-170) REVERT: F 112 LYS cc_start: 0.8297 (mttt) cc_final: 0.7966 (mttp) REVERT: F 174 ASN cc_start: 0.8407 (t0) cc_final: 0.7798 (t0) REVERT: F 205 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7499 (mp0) REVERT: F 397 ASP cc_start: 0.7526 (m-30) cc_final: 0.7176 (m-30) REVERT: F 400 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7445 (p) REVERT: F 451 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: D 249 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: D 390 ILE cc_start: 0.8050 (mt) cc_final: 0.7816 (mm) REVERT: D 475 LYS cc_start: 0.7379 (ttpt) cc_final: 0.7025 (tmtt) REVERT: G 233 ASP cc_start: 0.7882 (t70) cc_final: 0.7668 (t70) REVERT: O 136 THR cc_start: 0.7324 (m) cc_final: 0.7083 (p) outliers start: 48 outliers final: 24 residues processed: 333 average time/residue: 0.7039 time to fit residues: 263.8767 Evaluate side-chains 316 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 253 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 229 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN C 78 ASN C 215 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 42 GLN F 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098304 restraints weight = 31579.230| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.71 r_work: 0.3051 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24307 Z= 0.186 Angle : 0.546 11.153 32878 Z= 0.280 Chirality : 0.044 0.162 3827 Planarity : 0.004 0.044 4250 Dihedral : 6.479 142.965 3413 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 13.15 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.38 (0.15), residues: 3102 helix: 1.22 (0.14), residues: 1331 sheet: -0.54 (0.23), residues: 498 loop : -0.33 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 373 TYR 0.011 0.001 TYR O 170 PHE 0.019 0.001 PHE J 34 HIS 0.004 0.001 HIS D 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (24307) covalent geometry : angle 0.54607 / 0.28 (32878) hydrogen bonds : bond 0.04728 / 3.27 ( 1135) hydrogen bonds : angle 4.89220 / 3.37 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 305 time to evaluate : 0.703 Fit side-chains REVERT: A 355 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7978 (tt0) REVERT: B 67 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: B 124 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8296 (mppt) REVERT: B 353 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8068 (mm-30) REVERT: B 475 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: B 498 LYS cc_start: 0.7787 (ttmt) cc_final: 0.7157 (tptt) REVERT: C 124 LYS cc_start: 0.7864 (mmtm) cc_final: 0.7524 (mttm) REVERT: C 215 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8143 (mm110) REVERT: C 224 ASP cc_start: 0.8298 (t0) cc_final: 0.7599 (t0) REVERT: C 426 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: C 471 HIS cc_start: 0.5826 (t70) cc_final: 0.5117 (t-170) REVERT: E 29 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6791 (p0) REVERT: F 112 LYS cc_start: 0.8273 (mttt) cc_final: 0.7957 (mttp) REVERT: F 174 ASN cc_start: 0.8419 (t0) cc_final: 0.7817 (t0) REVERT: F 205 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7477 (mp0) REVERT: F 210 ASN cc_start: 0.8751 (t0) cc_final: 0.8391 (t0) REVERT: F 400 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7460 (p) REVERT: F 451 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: D 355 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8781 (t0) REVERT: D 475 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7058 (tmtt) REVERT: G 233 ASP cc_start: 0.7902 (t70) cc_final: 0.7683 (t70) REVERT: O 15 GLU cc_start: 0.7166 (mp0) cc_final: 0.6760 (mp0) REVERT: O 136 THR cc_start: 0.7305 (m) cc_final: 0.7076 (p) REVERT: O 168 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6831 (mt-10) outliers start: 55 outliers final: 30 residues processed: 339 average time/residue: 0.6956 time to fit residues: 265.8475 Evaluate side-chains 319 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 287 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN E 224 GLN E 445 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.099229 restraints weight = 31217.776| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.76 r_work: 0.3055 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24307 Z= 0.117 Angle : 0.497 11.929 32878 Z= 0.253 Chirality : 0.042 0.149 3827 Planarity : 0.004 0.041 4250 Dihedral : 6.170 141.932 3413 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Rotamer: Outliers : 1.81 % Allowed : 14.38 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.73 (0.15), residues: 3102 helix: 1.57 (0.14), residues: 1326 sheet: -0.37 (0.24), residues: 464 loop : -0.22 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 340 TYR 0.021 0.001 TYR B 446 PHE 0.017 0.001 PHE J 34 HIS 0.004 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (24307) covalent geometry : angle 0.49658 / 0.25 (32878) hydrogen bonds : bond 0.03975 / 2.75 ( 1135) hydrogen bonds : angle 4.70418 / 3.24 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.845 Fit side-chains REVERT: A 355 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7923 (tt0) REVERT: A 403 PHE cc_start: 0.7161 (m-80) cc_final: 0.6948 (m-80) REVERT: B 124 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8265 (mppt) REVERT: B 353 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8028 (mm-30) REVERT: B 498 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7087 (tptt) REVERT: C 124 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7445 (mttm) REVERT: C 224 ASP cc_start: 0.8347 (t0) cc_final: 0.7689 (t0) REVERT: C 301 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8919 (tp) REVERT: C 426 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: C 471 HIS cc_start: 0.5788 (t70) cc_final: 0.5042 (t-170) REVERT: E 128 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7528 (mm-30) REVERT: E 340 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.8009 (mtt-85) REVERT: E 458 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (mp-120) REVERT: F 112 LYS cc_start: 0.8276 (mttt) cc_final: 0.7968 (mttp) REVERT: F 174 ASN cc_start: 0.8369 (t0) cc_final: 0.7779 (t0) REVERT: F 205 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7413 (mp0) REVERT: F 210 ASN cc_start: 0.8698 (t0) cc_final: 0.8330 (t0) REVERT: F 217 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8168 (mptm) REVERT: F 400 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7418 (p) REVERT: F 451 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: D 205 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: D 249 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: D 475 LYS cc_start: 0.7400 (ttpt) cc_final: 0.7053 (tmtt) REVERT: G 233 ASP cc_start: 0.7872 (t70) cc_final: 0.7643 (t70) REVERT: O 15 GLU cc_start: 0.7070 (mp0) cc_final: 0.6562 (pt0) REVERT: O 136 THR cc_start: 0.7227 (m) cc_final: 0.6981 (p) outliers start: 46 outliers final: 19 residues processed: 347 average time/residue: 0.6603 time to fit residues: 258.7101 Evaluate side-chains 323 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 135 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 173 optimal weight: 0.1980 chunk 207 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 302 HIS A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN E 388 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092831 restraints weight = 31729.684| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.73 r_work: 0.2938 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 24307 Z= 0.287 Angle : 0.619 11.945 32878 Z= 0.316 Chirality : 0.048 0.184 3827 Planarity : 0.004 0.046 4250 Dihedral : 6.720 154.691 3413 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 2.24 % Allowed : 15.01 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.42 (0.15), residues: 3102 helix: 1.19 (0.14), residues: 1332 sheet: -0.45 (0.23), residues: 500 loop : -0.27 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 286 TYR 0.017 0.002 TYR B 446 PHE 0.020 0.002 PHE J 34 HIS 0.005 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.29 (24307) covalent geometry : angle 0.61899 / 0.32 (32878) hydrogen bonds : bond 0.05379 / 3.72 ( 1135) hydrogen bonds : angle 4.99352 / 3.44 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 0.967 Fit side-chains REVERT: A 355 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7902 (tt0) REVERT: B 67 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: B 353 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8064 (mm-30) REVERT: B 498 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7090 (tptt) REVERT: C 124 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7437 (mttm) REVERT: C 224 ASP cc_start: 0.8362 (t0) cc_final: 0.7617 (t0) REVERT: C 373 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7687 (mtt-85) REVERT: C 426 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: C 471 HIS cc_start: 0.5802 (t70) cc_final: 0.5088 (t-170) REVERT: E 29 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6825 (p0) REVERT: E 122 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: E 128 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: E 439 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: F 205 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7481 (mp0) REVERT: F 217 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8168 (mptm) REVERT: D 205 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: D 249 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: D 355 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8737 (t0) REVERT: D 475 LYS cc_start: 0.7364 (ttpt) cc_final: 0.6997 (tmtt) REVERT: G 233 ASP cc_start: 0.7859 (t70) cc_final: 0.7617 (t70) REVERT: O 15 GLU cc_start: 0.7053 (mp0) cc_final: 0.6612 (mp0) REVERT: O 136 THR cc_start: 0.7291 (m) cc_final: 0.7081 (p) REVERT: O 168 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6855 (mt-10) outliers start: 57 outliers final: 28 residues processed: 320 average time/residue: 0.6711 time to fit residues: 241.9474 Evaluate side-chains 321 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 438 LYS Chi-restraints excluded: chain E residue 439 GLU Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 355 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 221 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 HIS A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098257 restraints weight = 31436.435| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.76 r_work: 0.3043 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24307 Z= 0.112 Angle : 0.500 11.386 32878 Z= 0.254 Chirality : 0.042 0.153 3827 Planarity : 0.004 0.042 4250 Dihedral : 6.226 152.225 3413 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 1.89 % Allowed : 15.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 0.86 (0.15), residues: 3102 helix: 1.63 (0.14), residues: 1325 sheet: -0.13 (0.24), residues: 466 loop : -0.18 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.013 0.001 TYR A 446 PHE 0.018 0.001 PHE J 34 HIS 0.004 0.001 HIS E 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24307) covalent geometry : angle 0.49995 / 0.25 (32878) hydrogen bonds : bond 0.03910 / 2.70 ( 1135) hydrogen bonds : angle 4.71125 / 3.24 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.630 Fit side-chains REVERT: A 355 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7912 (tt0) REVERT: B 353 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8035 (mm-30) REVERT: B 498 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7035 (tptt) REVERT: C 124 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7442 (mttm) REVERT: C 224 ASP cc_start: 0.8330 (t0) cc_final: 0.7687 (t0) REVERT: C 426 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: C 471 HIS cc_start: 0.5793 (t70) cc_final: 0.5099 (t-170) REVERT: E 29 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6778 (p0) REVERT: E 340 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8122 (mtt-85) REVERT: F 112 LYS cc_start: 0.8290 (mttt) cc_final: 0.7990 (mttp) REVERT: F 174 ASN cc_start: 0.8360 (t0) cc_final: 0.7778 (t0) REVERT: F 205 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7449 (mp0) REVERT: F 210 ASN cc_start: 0.8644 (t0) cc_final: 0.8376 (t0) REVERT: F 217 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8159 (mptm) REVERT: F 400 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7426 (p) REVERT: D 205 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: D 249 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: D 475 LYS cc_start: 0.7399 (ttpt) cc_final: 0.7056 (tmtt) REVERT: G 233 ASP cc_start: 0.7879 (t70) cc_final: 0.7655 (t70) REVERT: O 15 GLU cc_start: 0.7029 (mp0) cc_final: 0.6592 (pt0) REVERT: O 103 SER cc_start: 0.7248 (t) cc_final: 0.6816 (p) REVERT: O 136 THR cc_start: 0.7345 (m) cc_final: 0.7106 (p) REVERT: O 168 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6889 (tt0) outliers start: 48 outliers final: 22 residues processed: 336 average time/residue: 0.6405 time to fit residues: 245.9648 Evaluate side-chains 325 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LYS Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 43 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 220 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN E 224 GLN F 27 GLN F 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098958 restraints weight = 31277.724| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.75 r_work: 0.3069 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24307 Z= 0.110 Angle : 0.495 10.929 32878 Z= 0.250 Chirality : 0.042 0.145 3827 Planarity : 0.003 0.042 4250 Dihedral : 6.107 153.694 3413 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.36 % Rotamer: Outliers : 1.61 % Allowed : 15.52 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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 (0.15), residues: 3102 helix: 1.82 (0.14), residues: 1325 sheet: -0.09 (0.24), residues: 470 loop : -0.05 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.021 0.001 TYR B 446 PHE 0.025 0.001 PHE C 468 HIS 0.016 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24307) covalent geometry : angle 0.49509 / 0.25 (32878) hydrogen bonds : bond 0.03835 / 2.65 ( 1135) hydrogen bonds : angle 4.61524 / 3.17 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8826 (tp) cc_final: 0.8582 (tt) REVERT: A 355 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7883 (tt0) REVERT: B 353 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8052 (mm-30) REVERT: B 415 GLN cc_start: 0.6719 (mt0) cc_final: 0.6187 (mt0) REVERT: B 498 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7177 (tmtt) REVERT: C 124 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7436 (mttm) REVERT: C 224 ASP cc_start: 0.8327 (t0) cc_final: 0.7692 (t0) REVERT: C 426 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: C 471 HIS cc_start: 0.5899 (t70) cc_final: 0.5223 (t-170) REVERT: E 29 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6782 (p0) REVERT: E 340 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.8089 (mtt-85) REVERT: F 112 LYS cc_start: 0.8300 (mttt) cc_final: 0.8014 (mttp) REVERT: F 174 ASN cc_start: 0.8352 (t0) cc_final: 0.7790 (t0) REVERT: F 202 GLU cc_start: 0.8558 (tt0) cc_final: 0.8310 (pt0) REVERT: F 205 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7424 (mp0) REVERT: F 210 ASN cc_start: 0.8594 (t0) cc_final: 0.8322 (t0) REVERT: F 400 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7412 (p) REVERT: F 408 SER cc_start: 0.8554 (t) cc_final: 0.8319 (p) REVERT: D 205 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: D 249 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: D 475 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6941 (tmtt) REVERT: G 233 ASP cc_start: 0.7858 (t70) cc_final: 0.7631 (t70) REVERT: O 15 GLU cc_start: 0.7013 (mp0) cc_final: 0.6649 (pt0) REVERT: O 136 THR cc_start: 0.7278 (m) cc_final: 0.6917 (p) REVERT: O 139 LYS cc_start: 0.6716 (ptmm) cc_final: 0.6015 (tptp) outliers start: 41 outliers final: 25 residues processed: 344 average time/residue: 0.6493 time to fit residues: 253.7125 Evaluate side-chains 330 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 217 optimal weight: 0.0870 chunk 247 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN B 385 GLN E 37 ASN E 224 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100679 restraints weight = 31439.278| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.77 r_work: 0.3095 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24307 Z= 0.097 Angle : 0.484 10.765 32878 Z= 0.245 Chirality : 0.042 0.142 3827 Planarity : 0.003 0.041 4250 Dihedral : 5.969 154.116 3413 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.64 % Favored : 98.32 % Rotamer: Outliers : 1.22 % Allowed : 16.42 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.26 (0.16), residues: 3102 helix: 1.99 (0.15), residues: 1320 sheet: -0.04 (0.24), residues: 469 loop : 0.07 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 373 TYR 0.022 0.001 TYR B 446 PHE 0.016 0.001 PHE J 34 HIS 0.015 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (24307) covalent geometry : angle 0.48377 / 0.24 (32878) hydrogen bonds : bond 0.03549 / 2.44 ( 1135) hydrogen bonds : angle 4.54714 / 3.13 ( 3231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 315 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7888 (tt0) REVERT: B 415 GLN cc_start: 0.6704 (mt0) cc_final: 0.6159 (mt0) REVERT: B 498 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7028 (tptt) REVERT: C 124 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7442 (mttm) REVERT: C 224 ASP cc_start: 0.8309 (t0) cc_final: 0.7707 (t0) REVERT: C 426 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: C 471 HIS cc_start: 0.5868 (t70) cc_final: 0.5165 (t-170) REVERT: E 29 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6841 (p0) REVERT: E 340 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.8063 (mtt-85) REVERT: F 112 LYS cc_start: 0.8307 (mttt) cc_final: 0.8023 (mttp) REVERT: F 174 ASN cc_start: 0.8297 (t0) cc_final: 0.7780 (t0) REVERT: F 202 GLU cc_start: 0.8541 (tt0) cc_final: 0.8301 (pt0) REVERT: F 205 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7372 (mp0) REVERT: F 388 GLN cc_start: 0.7597 (tp40) cc_final: 0.6929 (mm-40) REVERT: F 400 SER cc_start: 0.7853 (OUTLIER) cc_final: 0.7524 (p) REVERT: D 170 MET cc_start: 0.8353 (mmt) cc_final: 0.8005 (mmt) REVERT: D 205 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: D 453 ASP cc_start: 0.7888 (m-30) cc_final: 0.7395 (m-30) REVERT: D 475 LYS cc_start: 0.7240 (ttpt) cc_final: 0.6894 (tmtt) REVERT: G 233 ASP cc_start: 0.7812 (t70) cc_final: 0.7582 (t70) REVERT: G 241 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: O 15 GLU cc_start: 0.7053 (mp0) cc_final: 0.6681 (pt0) REVERT: O 136 THR cc_start: 0.7207 (m) cc_final: 0.6833 (p) REVERT: O 139 LYS cc_start: 0.6691 (ptmm) cc_final: 0.5870 (tptp) outliers start: 31 outliers final: 17 residues processed: 335 average time/residue: 0.6565 time to fit residues: 249.4570 Evaluate side-chains 325 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 295 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 264 optimal weight: 0.0980 chunk 193 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 210 ASN E 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096663 restraints weight = 31605.789| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.76 r_work: 0.3032 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24307 Z= 0.171 Angle : 0.549 10.486 32878 Z= 0.279 Chirality : 0.044 0.152 3827 Planarity : 0.004 0.043 4250 Dihedral : 6.337 158.932 3413 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 1.18 % Allowed : 16.74 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.03 (0.15), residues: 3102 helix: 1.75 (0.14), residues: 1331 sheet: -0.30 (0.24), residues: 478 loop : 0.05 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.021 0.001 TYR B 446 PHE 0.032 0.001 PHE C 468 HIS 0.017 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (24307) covalent geometry : angle 0.54902 / 0.28 (32878) hydrogen bonds : bond 0.04440 / 3.07 ( 1135) hydrogen bonds : angle 4.71691 / 3.25 ( 3231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 302 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7910 (tt0) REVERT: B 498 LYS cc_start: 0.7824 (ttmt) cc_final: 0.7116 (tptt) REVERT: C 124 LYS cc_start: 0.7803 (mmtm) cc_final: 0.7468 (mttm) REVERT: C 224 ASP cc_start: 0.8373 (t0) cc_final: 0.7693 (t0) REVERT: C 426 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: C 471 HIS cc_start: 0.5882 (t70) cc_final: 0.5173 (t-170) REVERT: E 29 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6882 (p0) REVERT: E 340 ARG cc_start: 0.8311 (mtp-110) cc_final: 0.8088 (mtt-85) REVERT: F 112 LYS cc_start: 0.8288 (mttt) cc_final: 0.8006 (mttp) REVERT: F 174 ASN cc_start: 0.8371 (t0) cc_final: 0.7839 (t0) REVERT: F 205 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7443 (mp0) REVERT: F 400 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7407 (p) REVERT: D 205 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: D 475 LYS cc_start: 0.7306 (ttpt) cc_final: 0.6952 (tmtt) REVERT: G 233 ASP cc_start: 0.7912 (t70) cc_final: 0.7683 (t70) REVERT: O 15 GLU cc_start: 0.7085 (mp0) cc_final: 0.6711 (pt0) REVERT: O 136 THR cc_start: 0.7317 (m) cc_final: 0.6971 (p) REVERT: O 139 LYS cc_start: 0.6736 (ptmm) cc_final: 0.5869 (tptp) outliers start: 30 outliers final: 18 residues processed: 318 average time/residue: 0.7236 time to fit residues: 260.1188 Evaluate side-chains 314 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 400 SER Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 201 optimal weight: 4.9990 chunk 252 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 268 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN E 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101528 restraints weight = 31274.537| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.76 r_work: 0.3088 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24307 Z= 0.102 Angle : 0.491 10.607 32878 Z= 0.248 Chirality : 0.042 0.143 3827 Planarity : 0.003 0.042 4250 Dihedral : 6.042 159.062 3413 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.68 % Favored : 98.29 % Rotamer: Outliers : 0.98 % Allowed : 16.86 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.26 (0.16), residues: 3102 helix: 1.98 (0.14), residues: 1319 sheet: -0.08 (0.24), residues: 483 loop : 0.11 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.022 0.001 TYR B 446 PHE 0.016 0.001 PHE J 34 HIS 0.019 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (24307) covalent geometry : angle 0.49104 / 0.25 (32878) hydrogen bonds : bond 0.03655 / 2.52 ( 1135) hydrogen bonds : angle 4.58300 / 3.15 ( 3231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8620.89 seconds wall clock time: 147 minutes 29.35 seconds (8849.35 seconds total)