Starting phenix.real_space_refine on Sat Jun 21 03:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh8_34755/06_2025/8hh8_34755.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.40, per 1000 atoms: 0.59 Number of scatterers: 24250 At special positions: 0 Unit cell: (127.6, 122.32, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 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: 6.14 Conformation dependent library (CDL) restraints added in 3.2 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 20 sheets defined 48.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.605A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.590A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.645A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.803A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.030A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.550A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.550A pdb=" N ASP A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.572A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.569A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.741A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.602A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.645A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.668A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.700A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.979A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.543A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.610A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.678A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.586A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.551A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.567A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.768A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.599A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 396 removed outlier: 3.702A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.539A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.512A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.509A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.970A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.604A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.179A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.831A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.592A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.038A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 5.142A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.824A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.530A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 380 removed outlier: 3.598A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.523A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.933A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.577A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.199A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.964A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.639A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.710A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 3.936A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.613A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 465 removed outlier: 3.527A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.711A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.972A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.562A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.550A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 221 removed outlier: 3.941A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 228 through 283 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.892A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.050A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.486A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.404A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.198A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.400A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.310A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.875A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.519A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.741A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.513A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.219A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.371A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.372A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.327A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.201A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.070A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3315 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: 8.44 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8226 1.34 - 1.46: 4591 1.46 - 1.58: 11666 1.58 - 1.70: 18 1.70 - 1.82: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N THR C 406 " pdb=" CA THR C 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 32920 1.85 - 3.70: 458 3.70 - 5.55: 46 5.55 - 7.40: 7 7.40 - 9.25: 2 Bond angle restraints: 33433 Sorted by residual: angle pdb=" C LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta sigma weight residual 110.79 103.92 6.87 1.66e+00 3.63e-01 1.71e+01 angle pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" C LYS C 409 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN C 407 " pdb=" CA GLN C 407 " pdb=" C GLN C 407 " ideal model delta sigma weight residual 111.28 107.45 3.83 1.09e+00 8.42e-01 1.23e+01 angle pdb=" C LEU D 455 " pdb=" N VAL D 456 " pdb=" CA VAL D 456 " ideal model delta sigma weight residual 123.08 119.89 3.19 1.01e+00 9.80e-01 9.97e+00 angle pdb=" C ILE G 225 " pdb=" N TYR G 226 " pdb=" CA TYR G 226 " ideal model delta sigma weight residual 122.79 117.44 5.35 1.70e+00 3.46e-01 9.90e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 14195 22.31 - 44.63: 689 44.63 - 66.94: 129 66.94 - 89.26: 44 89.26 - 111.57: 2 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PB ADP D 602 " pdb=" PA ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 -171.57 111.57 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" CA GLU G 222 " pdb=" C GLU G 222 " pdb=" N SER G 223 " pdb=" CA SER G 223 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C LYS C 409 " pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta harmonic sigma weight residual -122.60 -112.97 -9.63 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3248 0.059 - 0.117: 552 0.117 - 0.176: 49 0.176 - 0.234: 2 0.234 - 0.293: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA LYS C 409 " pdb=" N LYS C 409 " pdb=" C LYS C 409 " pdb=" CB LYS C 409 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 194 " pdb=" CB LEU G 194 " pdb=" CD1 LEU G 194 " pdb=" CD2 LEU G 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR G 226 " pdb=" N TYR G 226 " pdb=" C TYR G 226 " pdb=" CB TYR G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 110 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 221 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 221 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " -0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 113 2.57 - 3.15: 19253 3.15 - 3.73: 36384 3.73 - 4.32: 52466 4.32 - 4.90: 89186 Nonbonded interactions: 197402 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.010 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.058 2.170 ... (remaining 197397 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 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: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 54.490 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.090 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:15.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24655 Z= 0.148 Angle : 0.556 9.254 33433 Z= 0.319 Chirality : 0.044 0.293 3852 Planarity : 0.004 0.058 4362 Dihedral : 14.033 111.572 9347 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1260 sheet: 0.96 (0.23), residues: 536 loop : -0.12 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.014 0.001 PHE A 463 TYR 0.025 0.001 TYR G 226 ARG 0.003 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.15134 ( 1163) hydrogen bonds : angle 6.09360 ( 3315) covalent geometry : bond 0.00297 (24655) covalent geometry : angle 0.55620 (33433) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 3.357 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8126 (m-30) cc_final: 0.7835 (m-30) REVERT: E 1 MET cc_start: 0.5116 (ptm) cc_final: 0.4567 (ptm) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 1.5639 time to fit residues: 251.6011 Evaluate side-chains 98 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 266 GLN C 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.053316 restraints weight = 53619.153| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.31 r_work: 0.2662 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24655 Z= 0.195 Angle : 0.576 9.158 33433 Z= 0.301 Chirality : 0.046 0.285 3852 Planarity : 0.005 0.053 4362 Dihedral : 7.583 83.067 3546 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.78 % Allowed : 5.33 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3115 helix: 1.52 (0.15), residues: 1266 sheet: 0.63 (0.22), residues: 550 loop : -0.14 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 107 PHE 0.019 0.002 PHE D 257 TYR 0.021 0.001 TYR A 329 ARG 0.004 0.000 ARG G 240 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 1163) hydrogen bonds : angle 5.02223 ( 3315) covalent geometry : bond 0.00471 (24655) covalent geometry : angle 0.57566 (33433) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 2.895 Fit side-chains revert: symmetry clash REVERT: A 398 PHE cc_start: 0.7800 (m-10) cc_final: 0.7586 (m-10) REVERT: B 465 ASP cc_start: 0.8427 (m-30) cc_final: 0.8069 (m-30) REVERT: E 1 MET cc_start: 0.5448 (ptm) cc_final: 0.4938 (ptm) REVERT: F 1 MET cc_start: 0.8070 (tpp) cc_final: 0.7860 (tpp) REVERT: G 67 MET cc_start: 0.7412 (ptt) cc_final: 0.6861 (mmp) outliers start: 20 outliers final: 5 residues processed: 115 average time/residue: 1.4444 time to fit residues: 192.7530 Evaluate side-chains 97 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 467 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 292 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS D 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052515 restraints weight = 53400.575| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.32 r_work: 0.2642 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24655 Z= 0.210 Angle : 0.558 9.204 33433 Z= 0.292 Chirality : 0.046 0.244 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.457 86.140 3546 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.09 % Allowed : 6.89 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3115 helix: 1.49 (0.15), residues: 1276 sheet: 0.58 (0.22), residues: 549 loop : -0.21 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.019 0.002 PHE D 257 TYR 0.019 0.001 TYR A 329 ARG 0.005 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.05532 ( 1163) hydrogen bonds : angle 5.00574 ( 3315) covalent geometry : bond 0.00511 (24655) covalent geometry : angle 0.55829 (33433) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 2.897 Fit side-chains REVERT: B 465 ASP cc_start: 0.8493 (m-30) cc_final: 0.8072 (m-30) REVERT: E 1 MET cc_start: 0.5406 (ptm) cc_final: 0.4964 (ptm) REVERT: G 48 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4833 (tmtt) REVERT: G 67 MET cc_start: 0.7418 (ptt) cc_final: 0.6895 (mmt) outliers start: 28 outliers final: 9 residues processed: 113 average time/residue: 1.4298 time to fit residues: 189.8294 Evaluate side-chains 105 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 245 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 158 optimal weight: 0.3980 chunk 163 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053125 restraints weight = 53879.324| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.33 r_work: 0.2654 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24655 Z= 0.168 Angle : 0.523 8.842 33433 Z= 0.273 Chirality : 0.045 0.198 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.185 91.021 3546 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.29 % Allowed : 7.94 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3115 helix: 1.60 (0.15), residues: 1274 sheet: 0.57 (0.22), residues: 541 loop : -0.21 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 363 PHE 0.018 0.001 PHE D 257 TYR 0.014 0.001 TYR A 329 ARG 0.004 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 1163) hydrogen bonds : angle 4.86318 ( 3315) covalent geometry : bond 0.00404 (24655) covalent geometry : angle 0.52291 (33433) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 2.851 Fit side-chains REVERT: B 465 ASP cc_start: 0.8513 (m-30) cc_final: 0.8099 (m-30) REVERT: E 1 MET cc_start: 0.5368 (ptm) cc_final: 0.4930 (ptm) REVERT: F 1 MET cc_start: 0.8244 (tpp) cc_final: 0.7986 (tpp) REVERT: G 48 LYS cc_start: 0.5767 (OUTLIER) cc_final: 0.4831 (tmtt) REVERT: G 67 MET cc_start: 0.7532 (ptt) cc_final: 0.6955 (mtp) outliers start: 33 outliers final: 13 residues processed: 122 average time/residue: 1.6539 time to fit residues: 236.7141 Evaluate side-chains 109 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 149 optimal weight: 0.0270 chunk 21 optimal weight: 0.9980 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052670 restraints weight = 54007.159| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.34 r_work: 0.2644 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24655 Z= 0.187 Angle : 0.534 8.993 33433 Z= 0.279 Chirality : 0.045 0.170 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.159 92.919 3546 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.25 % Allowed : 8.96 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3115 helix: 1.57 (0.15), residues: 1275 sheet: 0.54 (0.22), residues: 541 loop : -0.22 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.019 0.002 PHE D 257 TYR 0.014 0.001 TYR A 329 ARG 0.003 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 1163) hydrogen bonds : angle 4.87189 ( 3315) covalent geometry : bond 0.00453 (24655) covalent geometry : angle 0.53435 (33433) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 3.056 Fit side-chains REVERT: B 465 ASP cc_start: 0.8545 (m-30) cc_final: 0.8105 (m-30) REVERT: E 1 MET cc_start: 0.5498 (ptm) cc_final: 0.5086 (ptm) REVERT: G 48 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.4848 (tmtt) REVERT: G 67 MET cc_start: 0.7573 (ptt) cc_final: 0.6997 (mtp) outliers start: 32 outliers final: 16 residues processed: 120 average time/residue: 1.2996 time to fit residues: 184.2694 Evaluate side-chains 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 58 optimal weight: 5.9990 chunk 170 optimal weight: 0.0980 chunk 214 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 25 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054759 restraints weight = 53257.989| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.33 r_work: 0.2695 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24655 Z= 0.107 Angle : 0.476 9.395 33433 Z= 0.246 Chirality : 0.043 0.144 3852 Planarity : 0.004 0.045 4362 Dihedral : 6.790 86.404 3546 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.13 % Allowed : 9.50 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3115 helix: 1.86 (0.15), residues: 1270 sheet: 0.66 (0.22), residues: 534 loop : -0.12 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.014 0.001 PHE D 257 TYR 0.010 0.001 TYR A 248 ARG 0.004 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 1163) hydrogen bonds : angle 4.63683 ( 3315) covalent geometry : bond 0.00240 (24655) covalent geometry : angle 0.47631 (33433) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 2.837 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8495 (m-30) cc_final: 0.8068 (m-30) REVERT: E 1 MET cc_start: 0.5371 (ptm) cc_final: 0.4973 (ptm) REVERT: F 1 MET cc_start: 0.8163 (tpp) cc_final: 0.7817 (tpp) REVERT: G 46 MET cc_start: 0.8335 (tpt) cc_final: 0.8123 (tpp) REVERT: G 67 MET cc_start: 0.7504 (ptt) cc_final: 0.7018 (mtp) outliers start: 29 outliers final: 14 residues processed: 117 average time/residue: 1.4205 time to fit residues: 196.5023 Evaluate side-chains 110 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 204 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 214 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.051799 restraints weight = 54184.258| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.34 r_work: 0.2624 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24655 Z= 0.247 Angle : 0.574 9.504 33433 Z= 0.299 Chirality : 0.047 0.188 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.172 93.035 3546 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.13 % Allowed : 9.93 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3115 helix: 1.55 (0.15), residues: 1273 sheet: 0.51 (0.22), residues: 542 loop : -0.23 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.021 0.002 PHE D 257 TYR 0.018 0.001 TYR G 226 ARG 0.004 0.000 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.05633 ( 1163) hydrogen bonds : angle 4.94024 ( 3315) covalent geometry : bond 0.00601 (24655) covalent geometry : angle 0.57434 (33433) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 2.792 Fit side-chains REVERT: B 465 ASP cc_start: 0.8596 (m-30) cc_final: 0.8131 (m-30) REVERT: C 375 MET cc_start: 0.9296 (mmt) cc_final: 0.9055 (mmt) REVERT: C 404 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8267 (mtpp) REVERT: E 1 MET cc_start: 0.5430 (ptm) cc_final: 0.5047 (ptm) REVERT: F 1 MET cc_start: 0.8262 (tpp) cc_final: 0.7984 (tpp) REVERT: G 48 LYS cc_start: 0.5817 (OUTLIER) cc_final: 0.4822 (tmtt) REVERT: G 67 MET cc_start: 0.7652 (ptt) cc_final: 0.7347 (tpt) REVERT: G 226 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7279 (m-80) outliers start: 29 outliers final: 18 residues processed: 117 average time/residue: 1.5866 time to fit residues: 217.0654 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 226 TYR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 97 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055017 restraints weight = 53311.798| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.33 r_work: 0.2701 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24655 Z= 0.101 Angle : 0.472 8.859 33433 Z= 0.244 Chirality : 0.042 0.141 3852 Planarity : 0.004 0.044 4362 Dihedral : 6.703 88.030 3546 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.86 % Allowed : 10.40 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3115 helix: 1.89 (0.15), residues: 1270 sheet: 0.66 (0.22), residues: 534 loop : -0.14 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.013 0.001 PHE D 125 TYR 0.010 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1163) hydrogen bonds : angle 4.61944 ( 3315) covalent geometry : bond 0.00225 (24655) covalent geometry : angle 0.47176 (33433) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 3.610 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8504 (m-30) cc_final: 0.8071 (m-30) REVERT: C 404 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8254 (mtpp) REVERT: E 1 MET cc_start: 0.5349 (ptm) cc_final: 0.4976 (ptm) REVERT: E 10 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8163 (mmm) REVERT: F 1 MET cc_start: 0.8178 (tpp) cc_final: 0.7890 (tpp) REVERT: G 46 MET cc_start: 0.8346 (tpt) cc_final: 0.8127 (tpp) REVERT: G 67 MET cc_start: 0.7657 (ptt) cc_final: 0.7334 (tpt) REVERT: G 68 LEU cc_start: 0.8388 (tm) cc_final: 0.8145 (mm) REVERT: G 226 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6984 (m-80) outliers start: 22 outliers final: 12 residues processed: 116 average time/residue: 2.6069 time to fit residues: 368.5105 Evaluate side-chains 111 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 6.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 139 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053881 restraints weight = 53818.834| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.33 r_work: 0.2673 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24655 Z= 0.142 Angle : 0.496 9.013 33433 Z= 0.257 Chirality : 0.044 0.147 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.728 83.684 3546 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.78 % Allowed : 10.51 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3115 helix: 1.85 (0.15), residues: 1270 sheet: 0.64 (0.23), residues: 519 loop : -0.17 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.016 0.001 PHE D 257 TYR 0.015 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 1163) hydrogen bonds : angle 4.66493 ( 3315) covalent geometry : bond 0.00339 (24655) covalent geometry : angle 0.49589 (33433) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 2.773 Fit side-chains REVERT: B 465 ASP cc_start: 0.8544 (m-30) cc_final: 0.8097 (m-30) REVERT: C 404 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8260 (mtpp) REVERT: E 1 MET cc_start: 0.5362 (ptm) cc_final: 0.4989 (ptm) REVERT: E 10 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: G 46 MET cc_start: 0.8365 (tpt) cc_final: 0.8151 (tpp) REVERT: G 67 MET cc_start: 0.7617 (ptt) cc_final: 0.7328 (tpt) REVERT: G 68 LEU cc_start: 0.8410 (tm) cc_final: 0.8206 (mm) REVERT: G 192 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8346 (t) outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 1.3496 time to fit residues: 181.9901 Evaluate side-chains 114 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 14 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 279 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055211 restraints weight = 53408.147| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.32 r_work: 0.2705 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24655 Z= 0.105 Angle : 0.472 10.919 33433 Z= 0.242 Chirality : 0.042 0.144 3852 Planarity : 0.004 0.045 4362 Dihedral : 6.529 86.669 3546 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.74 % Allowed : 10.51 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.15), residues: 3115 helix: 2.00 (0.15), residues: 1262 sheet: 0.68 (0.23), residues: 524 loop : -0.10 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.013 0.001 PHE D 257 TYR 0.012 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1163) hydrogen bonds : angle 4.56154 ( 3315) covalent geometry : bond 0.00237 (24655) covalent geometry : angle 0.47163 (33433) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 2.961 Fit side-chains REVERT: B 465 ASP cc_start: 0.8512 (m-30) cc_final: 0.8072 (m-30) REVERT: C 404 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8283 (mtpp) REVERT: E 1 MET cc_start: 0.5328 (ptm) cc_final: 0.4937 (ptm) REVERT: E 10 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8093 (mmm) REVERT: F 1 MET cc_start: 0.8145 (tpp) cc_final: 0.7821 (tpp) REVERT: G 46 MET cc_start: 0.8349 (tpt) cc_final: 0.8140 (tpp) REVERT: G 67 MET cc_start: 0.7625 (ptt) cc_final: 0.7316 (tpt) REVERT: G 68 LEU cc_start: 0.8422 (tm) cc_final: 0.8220 (mm) REVERT: G 130 ASN cc_start: 0.8380 (m110) cc_final: 0.8121 (m-40) REVERT: G 192 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8401 (t) outliers start: 19 outliers final: 15 residues processed: 119 average time/residue: 1.3623 time to fit residues: 190.3639 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 153 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.053332 restraints weight = 53837.489| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.33 r_work: 0.2669 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24655 Z= 0.170 Angle : 0.522 10.925 33433 Z= 0.269 Chirality : 0.044 0.169 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.712 84.726 3546 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.70 % Allowed : 10.90 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3115 helix: 1.84 (0.15), residues: 1268 sheet: 0.62 (0.22), residues: 519 loop : -0.14 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.018 0.001 PHE D 257 TYR 0.021 0.001 TYR G 226 ARG 0.002 0.000 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1163) hydrogen bonds : angle 4.70740 ( 3315) covalent geometry : bond 0.00412 (24655) covalent geometry : angle 0.52185 (33433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14896.29 seconds wall clock time: 265 minutes 4.53 seconds (15904.53 seconds total)