Starting phenix.real_space_refine on Thu Mar 5 18:25:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhb_34758/03_2026/8hhb_34758.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24245 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: 5.61, per 1000 atoms: 0.23 Number of scatterers: 24245 At special positions: 0 Unit cell: (128.48, 120.56, 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 15 15.00 Mg 5 11.99 O 4657 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 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: 132 helices and 21 sheets defined 48.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.529A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.936A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.650A 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 251 removed outlier: 3.777A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.655A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.193A 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 289 through 299 removed outlier: 3.646A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.923A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.561A pdb=" N ALA A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.604A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.652A 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: 3.563A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.699A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.614A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.817A 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 289 through 299 removed outlier: 3.785A 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 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.581A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.891A pdb=" N LEU B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.637A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.616A pdb=" N ASP B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.756A 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 185 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.695A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.693A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.511A pdb=" N SER C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.699A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 4.426A pdb=" N GLN C 397 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 399 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.615A pdb=" N GLN C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.712A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.597A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.505A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.559A 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 180 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.645A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.697A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.156A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.522A pdb=" N GLY D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 379 removed outlier: 3.694A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 411 removed outlier: 3.766A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D 411 " --> pdb=" O GLN D 407 " (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: 3.625A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 244 removed outlier: 3.621A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.946A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.550A 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 381 Processing helix chain 'E' and resid 383 through 388 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.901A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.673A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.563A 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 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: 4.731A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.083A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.620A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.671A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 removed outlier: 3.686A pdb=" N LEU F 325 " --> pdb=" O PHE F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 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 393 through 410 removed outlier: 3.720A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 4.001A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 4.032A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.993A pdb=" N THR G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 3.520A pdb=" N VAL G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.780A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 4.019A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 161 removed outlier: 3.679A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 208 through 284 removed outlier: 3.989A pdb=" N ILE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.578A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.807A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.898A 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: 4.249A 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: 3.637A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N GLN A 341 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N GLY A 360 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A 343 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.738A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.054A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.737A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.357A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 76 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY C 61 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.672A 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: 6.500A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 318 through 320 removed outlier: 8.097A pdb=" N VAL C 319 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.697A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.472A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLN D 217 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.495A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 5.991A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.681A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.778A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.204A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.569A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE G 81 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 186 " --> pdb=" O MET G 170 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 2.88 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: 8232 1.34 - 1.46: 4728 1.46 - 1.58: 11523 1.58 - 1.70: 14 1.70 - 1.82: 154 Bond restraints: 24651 Sorted by residual: bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.505 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C HIS G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.90e-03 1.26e+04 3.71e+00 ... (remaining 24646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 32633 1.74 - 3.48: 698 3.48 - 5.21: 83 5.21 - 6.95: 10 6.95 - 8.69: 3 Bond angle restraints: 33427 Sorted by residual: angle pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" C VAL A 25 " ideal model delta sigma weight residual 113.20 108.54 4.66 9.60e-01 1.09e+00 2.35e+01 angle pdb=" CA GLY F 298 " pdb=" C GLY F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 114.58 117.48 -2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N VAL D 275 " pdb=" CA VAL D 275 " pdb=" C VAL D 275 " ideal model delta sigma weight residual 111.77 108.31 3.46 1.04e+00 9.25e-01 1.11e+01 angle pdb=" C GLY D 443 " pdb=" N LYS D 444 " pdb=" CA LYS D 444 " ideal model delta sigma weight residual 122.55 115.83 6.72 2.03e+00 2.43e-01 1.09e+01 angle pdb=" N ASP B 262 " pdb=" CA ASP B 262 " pdb=" C ASP B 262 " ideal model delta sigma weight residual 107.32 112.58 -5.26 1.65e+00 3.67e-01 1.02e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 14066 21.25 - 42.50: 811 42.50 - 63.74: 125 63.74 - 84.99: 45 84.99 - 106.24: 12 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PB ADP D 603 " pdb=" PA ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 -166.24 106.24 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" CA GLU G 204 " pdb=" C GLU G 204 " pdb=" N PHE G 205 " pdb=" CA PHE G 205 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR G 203 " pdb=" C TYR G 203 " pdb=" N GLU G 204 " pdb=" CA GLU G 204 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2613 0.041 - 0.082: 873 0.082 - 0.123: 332 0.123 - 0.165: 32 0.165 - 0.206: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA PRO B 482 " pdb=" N PRO B 482 " pdb=" C PRO B 482 " pdb=" CB PRO B 482 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL D 87 " pdb=" CA VAL D 87 " pdb=" CG1 VAL D 87 " pdb=" CG2 VAL D 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA LEU G 189 " pdb=" N LEU G 189 " pdb=" C LEU G 189 " pdb=" CB LEU G 189 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 109 " -0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO G 110 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO G 110 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 110 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 481 " -0.063 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 482 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 482 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 482 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 409 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C LYS B 409 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS B 409 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 410 " 0.011 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 103 2.51 - 3.10: 17926 3.10 - 3.70: 36317 3.70 - 4.30: 52115 4.30 - 4.90: 89705 Nonbonded interactions: 196166 Sorted by model distance: nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.908 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.912 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 602 " model vdw 1.953 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 1.962 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.004 2.170 ... (remaining 196161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = chain 'E' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24651 Z= 0.190 Angle : 0.628 8.689 33427 Z= 0.356 Chirality : 0.046 0.206 3852 Planarity : 0.005 0.094 4362 Dihedral : 14.333 106.240 9347 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1242 sheet: 0.76 (0.22), residues: 556 loop : -0.05 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 140 TYR 0.019 0.002 TYR C 329 PHE 0.030 0.001 PHE G 205 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00431 (24651) covalent geometry : angle 0.62782 (33427) hydrogen bonds : bond 0.14896 ( 1165) hydrogen bonds : angle 6.30377 ( 3336) *********************** 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 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: B 272 GLU cc_start: 0.7994 (tt0) cc_final: 0.7706 (tp30) REVERT: D 56 ASP cc_start: 0.7182 (t0) cc_final: 0.6741 (t0) REVERT: F 74 MET cc_start: 0.8794 (mtt) cc_final: 0.8544 (mtt) REVERT: F 170 GLU cc_start: 0.8041 (tp30) cc_final: 0.7777 (tp30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1487 time to fit residues: 39.0228 Evaluate side-chains 131 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN C 474 HIS D 253 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.080152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.063673 restraints weight = 60450.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065801 restraints weight = 30703.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.067220 restraints weight = 19285.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068162 restraints weight = 13922.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068783 restraints weight = 11057.115| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24651 Z= 0.189 Angle : 0.580 8.144 33427 Z= 0.306 Chirality : 0.046 0.180 3852 Planarity : 0.005 0.066 4362 Dihedral : 7.864 88.285 3546 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.31 % Allowed : 4.98 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3115 helix: 1.50 (0.15), residues: 1238 sheet: 0.58 (0.22), residues: 556 loop : -0.15 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 140 TYR 0.015 0.001 TYR C 329 PHE 0.015 0.001 PHE G 205 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00452 (24651) covalent geometry : angle 0.58023 (33427) hydrogen bonds : bond 0.04990 ( 1165) hydrogen bonds : angle 5.19742 ( 3336) *********************** 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 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.841 Fit side-chains REVERT: B 48 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8654 (ptp) REVERT: D 56 ASP cc_start: 0.7197 (t0) cc_final: 0.6650 (t0) REVERT: F 170 GLU cc_start: 0.8275 (tp30) cc_final: 0.7858 (tp30) REVERT: G 241 MET cc_start: 0.6415 (ttt) cc_final: 0.6145 (tpp) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.1464 time to fit residues: 35.2249 Evaluate side-chains 134 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 287 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.062376 restraints weight = 60885.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064463 restraints weight = 30970.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.065846 restraints weight = 19534.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.066771 restraints weight = 14218.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067375 restraints weight = 11330.975| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24651 Z= 0.249 Angle : 0.617 9.764 33427 Z= 0.324 Chirality : 0.048 0.156 3852 Planarity : 0.005 0.065 4362 Dihedral : 7.711 83.956 3546 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.05 % Allowed : 7.79 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1232 sheet: 0.32 (0.21), residues: 556 loop : -0.34 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 164 TYR 0.017 0.002 TYR G 78 PHE 0.016 0.002 PHE A 494 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00602 (24651) covalent geometry : angle 0.61745 (33427) hydrogen bonds : bond 0.05283 ( 1165) hydrogen bonds : angle 5.14786 ( 3336) *********************** 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 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.937 Fit side-chains REVERT: C 210 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: D 56 ASP cc_start: 0.7238 (t0) cc_final: 0.6702 (t0) REVERT: F 170 GLU cc_start: 0.8225 (tp30) cc_final: 0.7674 (tp30) REVERT: F 213 MET cc_start: 0.8365 (mtp) cc_final: 0.7932 (mtm) REVERT: G 106 ARG cc_start: 0.6961 (ttm110) cc_final: 0.6626 (ttm110) outliers start: 27 outliers final: 11 residues processed: 151 average time/residue: 0.1396 time to fit residues: 35.3978 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 115 optimal weight: 0.6980 chunk 249 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 182 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 282 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN G 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.082018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066003 restraints weight = 59821.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068066 restraints weight = 31042.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.069423 restraints weight = 19713.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070335 restraints weight = 14369.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070933 restraints weight = 11496.656| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24651 Z= 0.095 Angle : 0.495 8.715 33427 Z= 0.258 Chirality : 0.043 0.156 3852 Planarity : 0.004 0.053 4362 Dihedral : 7.160 83.391 3546 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.93 % Allowed : 8.57 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3115 helix: 1.74 (0.15), residues: 1241 sheet: 0.56 (0.21), residues: 554 loop : -0.18 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 3 TYR 0.011 0.001 TYR G 78 PHE 0.011 0.001 PHE G 205 HIS 0.004 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00197 (24651) covalent geometry : angle 0.49461 (33427) hydrogen bonds : bond 0.03786 ( 1165) hydrogen bonds : angle 4.72944 ( 3336) *********************** 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 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.935 Fit side-chains REVERT: A 397 GLN cc_start: 0.4392 (OUTLIER) cc_final: 0.3582 (pm20) REVERT: C 436 ILE cc_start: 0.9155 (tp) cc_final: 0.8945 (tp) REVERT: D 56 ASP cc_start: 0.7063 (t0) cc_final: 0.6562 (t0) REVERT: D 74 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8718 (mtt) REVERT: F 74 MET cc_start: 0.8911 (mtt) cc_final: 0.8710 (mtt) REVERT: F 170 GLU cc_start: 0.8112 (tp30) cc_final: 0.7665 (tp30) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.1347 time to fit residues: 37.1958 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 94 optimal weight: 9.9990 chunk 266 optimal weight: 0.7980 chunk 299 optimal weight: 8.9990 chunk 219 optimal weight: 0.0370 chunk 77 optimal weight: 4.9990 chunk 131 optimal weight: 0.0870 chunk 60 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.064802 restraints weight = 60042.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066941 restraints weight = 30239.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068348 restraints weight = 18935.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069292 restraints weight = 13712.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069880 restraints weight = 10895.355| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24651 Z= 0.120 Angle : 0.499 8.595 33427 Z= 0.259 Chirality : 0.043 0.151 3852 Planarity : 0.004 0.053 4362 Dihedral : 7.011 86.171 3546 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.13 % Allowed : 9.54 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3115 helix: 1.80 (0.15), residues: 1236 sheet: 0.60 (0.22), residues: 556 loop : -0.13 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 3 TYR 0.014 0.001 TYR G 169 PHE 0.010 0.001 PHE A 494 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00277 (24651) covalent geometry : angle 0.49863 (33427) hydrogen bonds : bond 0.03952 ( 1165) hydrogen bonds : angle 4.66548 ( 3336) *********************** 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 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 397 GLN cc_start: 0.4333 (OUTLIER) cc_final: 0.3555 (pm20) REVERT: B 272 GLU cc_start: 0.7933 (tt0) cc_final: 0.7648 (tt0) REVERT: C 210 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: D 56 ASP cc_start: 0.7194 (t0) cc_final: 0.6620 (t0) REVERT: D 74 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8673 (mtt) REVERT: E 275 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8817 (t) REVERT: F 74 MET cc_start: 0.8977 (mtt) cc_final: 0.8670 (mtt) REVERT: F 170 GLU cc_start: 0.8167 (tp30) cc_final: 0.7583 (tp30) outliers start: 29 outliers final: 17 residues processed: 161 average time/residue: 0.1394 time to fit residues: 38.0978 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 183 optimal weight: 0.0270 chunk 298 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 86 optimal weight: 0.0270 chunk 153 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.1500 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.082452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066378 restraints weight = 59558.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068428 restraints weight = 30958.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.069779 restraints weight = 19761.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070696 restraints weight = 14430.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071296 restraints weight = 11553.549| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24651 Z= 0.097 Angle : 0.478 8.614 33427 Z= 0.248 Chirality : 0.043 0.219 3852 Planarity : 0.004 0.050 4362 Dihedral : 6.814 89.195 3546 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.32 % Allowed : 9.62 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3115 helix: 1.92 (0.15), residues: 1236 sheet: 0.75 (0.22), residues: 534 loop : -0.07 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 405 TYR 0.012 0.001 TYR B 389 PHE 0.010 0.001 PHE B 456 HIS 0.004 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00215 (24651) covalent geometry : angle 0.47845 (33427) hydrogen bonds : bond 0.03599 ( 1165) hydrogen bonds : angle 4.56057 ( 3336) *********************** 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 178 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.928 Fit side-chains REVERT: B 272 GLU cc_start: 0.7879 (tt0) cc_final: 0.7650 (tt0) REVERT: C 109 ASN cc_start: 0.8299 (t0) cc_final: 0.8029 (t0) REVERT: D 56 ASP cc_start: 0.7077 (t0) cc_final: 0.6557 (t0) REVERT: D 74 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8676 (mtt) REVERT: D 271 MET cc_start: 0.8642 (mmm) cc_final: 0.8001 (mtt) REVERT: E 275 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8819 (t) REVERT: F 74 MET cc_start: 0.8919 (mtt) cc_final: 0.8649 (mtt) REVERT: F 170 GLU cc_start: 0.8090 (tp30) cc_final: 0.7616 (tp30) outliers start: 34 outliers final: 22 residues processed: 169 average time/residue: 0.1353 time to fit residues: 38.9072 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 305 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN D 253 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.061783 restraints weight = 61034.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.063834 restraints weight = 31238.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065185 restraints weight = 19812.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.066090 restraints weight = 14419.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.066706 restraints weight = 11545.499| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 24651 Z= 0.317 Angle : 0.672 11.514 33427 Z= 0.348 Chirality : 0.050 0.237 3852 Planarity : 0.005 0.066 4362 Dihedral : 7.319 79.135 3546 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.71 % Allowed : 10.28 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1234 sheet: 0.45 (0.22), residues: 529 loop : -0.38 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 72 TYR 0.019 0.002 TYR G 78 PHE 0.020 0.002 PHE A 494 HIS 0.006 0.002 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00763 (24651) covalent geometry : angle 0.67212 (33427) hydrogen bonds : bond 0.05447 ( 1165) hydrogen bonds : angle 5.05474 ( 3336) *********************** 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 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.871 Fit side-chains REVERT: C 407 GLN cc_start: 0.6793 (pm20) cc_final: 0.6428 (mp10) REVERT: D 56 ASP cc_start: 0.7419 (t0) cc_final: 0.6782 (t0) REVERT: D 74 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8724 (mtt) REVERT: F 74 MET cc_start: 0.8931 (mtt) cc_final: 0.8608 (mtt) REVERT: F 170 GLU cc_start: 0.8233 (tp30) cc_final: 0.7629 (tp30) REVERT: G 216 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6337 (tp) outliers start: 44 outliers final: 30 residues processed: 163 average time/residue: 0.1315 time to fit residues: 36.5305 Evaluate side-chains 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 245 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 363 HIS ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064748 restraints weight = 59791.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.066881 restraints weight = 30159.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068307 restraints weight = 18863.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069237 restraints weight = 13562.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.069848 restraints weight = 10777.747| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24651 Z= 0.109 Angle : 0.516 8.619 33427 Z= 0.267 Chirality : 0.044 0.158 3852 Planarity : 0.004 0.056 4362 Dihedral : 6.965 78.622 3546 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.25 % Allowed : 10.98 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1237 sheet: 0.64 (0.22), residues: 536 loop : -0.25 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 120 TYR 0.013 0.001 TYR A 251 PHE 0.018 0.001 PHE A 395 HIS 0.004 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00239 (24651) covalent geometry : angle 0.51599 (33427) hydrogen bonds : bond 0.04041 ( 1165) hydrogen bonds : angle 4.71554 ( 3336) *********************** 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 165 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.005 Fit side-chains REVERT: B 272 GLU cc_start: 0.7979 (tt0) cc_final: 0.7725 (tt0) REVERT: D 56 ASP cc_start: 0.7311 (t0) cc_final: 0.6669 (t0) REVERT: D 74 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8636 (mtt) REVERT: F 1 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5485 (tpp) REVERT: F 74 MET cc_start: 0.8926 (mtt) cc_final: 0.8562 (mtt) REVERT: F 170 GLU cc_start: 0.8176 (tp30) cc_final: 0.7599 (tp30) REVERT: G 216 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6358 (tp) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.1337 time to fit residues: 35.7057 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 146 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 279 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 114 optimal weight: 0.4980 chunk 290 optimal weight: 8.9990 chunk 295 optimal weight: 30.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.062063 restraints weight = 61025.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.064120 restraints weight = 31175.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.065485 restraints weight = 19729.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066394 restraints weight = 14345.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.067003 restraints weight = 11473.032| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 24651 Z= 0.279 Angle : 0.637 9.049 33427 Z= 0.331 Chirality : 0.048 0.292 3852 Planarity : 0.005 0.063 4362 Dihedral : 7.185 82.016 3546 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.40 % Allowed : 10.94 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3115 helix: 1.38 (0.15), residues: 1233 sheet: 0.40 (0.22), residues: 530 loop : -0.43 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 333 TYR 0.017 0.002 TYR G 78 PHE 0.018 0.002 PHE A 494 HIS 0.010 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00670 (24651) covalent geometry : angle 0.63702 (33427) hydrogen bonds : bond 0.05191 ( 1165) hydrogen bonds : angle 4.99594 ( 3336) *********************** 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 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.831 Fit side-chains REVERT: A 250 MET cc_start: 0.8501 (tpp) cc_final: 0.8044 (ttm) REVERT: C 407 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: D 56 ASP cc_start: 0.7423 (t0) cc_final: 0.6792 (t0) REVERT: D 74 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8678 (mtt) REVERT: F 1 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5318 (tpp) REVERT: F 74 MET cc_start: 0.8947 (mtt) cc_final: 0.8593 (mtt) REVERT: F 170 GLU cc_start: 0.8254 (tp30) cc_final: 0.7639 (tp30) REVERT: G 216 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6378 (tp) outliers start: 36 outliers final: 28 residues processed: 151 average time/residue: 0.1335 time to fit residues: 34.7243 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 226 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 301 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.062465 restraints weight = 60538.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.064542 restraints weight = 30757.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.065900 restraints weight = 19351.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.066822 restraints weight = 14059.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067427 restraints weight = 11221.116| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 24651 Z= 0.198 Angle : 0.747 59.197 33427 Z= 0.411 Chirality : 0.046 0.279 3852 Planarity : 0.005 0.064 4362 Dihedral : 7.185 82.200 3546 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 11.14 % Favored : 87.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1232 sheet: 0.37 (0.22), residues: 530 loop : -0.42 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.017 0.002 TYR G 78 PHE 0.017 0.001 PHE A 494 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00453 (24651) covalent geometry : angle 0.74658 (33427) hydrogen bonds : bond 0.05033 ( 1165) hydrogen bonds : angle 4.98303 ( 3336) ********************** 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 153 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.972 Fit side-chains REVERT: A 250 MET cc_start: 0.8482 (tpp) cc_final: 0.8000 (ttm) REVERT: C 407 GLN cc_start: 0.6811 (pm20) cc_final: 0.6419 (mp10) REVERT: D 56 ASP cc_start: 0.7409 (t0) cc_final: 0.6788 (t0) REVERT: D 74 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8647 (mtt) REVERT: F 1 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5346 (tpp) REVERT: F 74 MET cc_start: 0.8943 (mtt) cc_final: 0.8585 (mtt) REVERT: F 170 GLU cc_start: 0.8249 (tp30) cc_final: 0.7627 (tp30) REVERT: G 216 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6378 (tp) outliers start: 31 outliers final: 27 residues processed: 148 average time/residue: 0.1256 time to fit residues: 31.9199 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 136 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.062451 restraints weight = 60610.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.064519 restraints weight = 30894.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065892 restraints weight = 19526.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.066805 restraints weight = 14188.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067363 restraints weight = 11325.621| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 24651 Z= 0.198 Angle : 0.747 59.197 33427 Z= 0.411 Chirality : 0.046 0.279 3852 Planarity : 0.005 0.064 4362 Dihedral : 7.185 82.200 3546 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.21 % Allowed : 11.06 % Favored : 87.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1232 sheet: 0.37 (0.22), residues: 530 loop : -0.42 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.017 0.002 TYR G 78 PHE 0.017 0.001 PHE A 494 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00453 (24651) covalent geometry : angle 0.74658 (33427) hydrogen bonds : bond 0.05033 ( 1165) hydrogen bonds : angle 4.98303 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.25 seconds wall clock time: 52 minutes 6.27 seconds (3126.27 seconds total)