Starting phenix.real_space_refine on Sun Jul 5 00:28:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhb_34758/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhb_34758/07_2026/8hhb_34758.cif" } 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-6108/lib/python3.11/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: 4.89, per 1000 atoms: 0.20 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: 1.52 Conformation dependent library (CDL) restraints added in 888.8 milliseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 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: 0.65 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: 4.04 Time building geometry restraints manager: 2.02 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: 14011 21.25 - 42.50: 772 42.50 - 63.74: 101 63.74 - 84.99: 41 84.99 - 106.24: 10 Dihedral angle restraints: 14935 sinusoidal: 6010 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 14932 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 19.520 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 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 : 13.843 106.240 9223 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/Z covalent geometry : bond 0.00431 / 0.19 (24651) covalent geometry : angle 0.62782 / 0.36 (33427) hydrogen bonds : bond 0.14896 / 10.09 ( 1165) hydrogen bonds : angle 6.30377 / 4.59 ( 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 : 1.008 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: 0.1612 time to fit residues: 42.7292 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 : 0.963 ------------------------------------------------------------------------------- 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... 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 = 0.080176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.063626 restraints weight = 60566.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.065766 restraints weight = 30829.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.067187 restraints weight = 19385.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068120 restraints weight = 14027.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068740 restraints weight = 11181.669| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0632 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 : 0.579 7.935 33427 Z= 0.305 Chirality : 0.046 0.183 3852 Planarity : 0.005 0.066 4362 Dihedral : 5.669 89.776 3422 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.27 % Allowed : 5.02 % 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 0.005 0.000 ARG B 140 TYR 0.014 0.001 TYR G 78 PHE 0.015 0.001 PHE G 205 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (24651) covalent geometry : angle 0.57949 / 0.31 (33427) hydrogen bonds : bond 0.04982 / 3.39 ( 1165) hydrogen bonds : angle 5.22600 / 3.77 ( 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 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.048 Fit side-chains REVERT: D 56 ASP cc_start: 0.7197 (t0) cc_final: 0.6648 (t0) REVERT: F 170 GLU cc_start: 0.8277 (tp30) cc_final: 0.7861 (tp30) REVERT: G 241 MET cc_start: 0.6400 (ttt) cc_final: 0.6174 (tpp) outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.1594 time to fit residues: 38.1615 Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 30.0000 chunk 211 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 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: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 GLN ** 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 = 0.3137 r_free = 0.3137 target = 0.078128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.061749 restraints weight = 61169.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.063816 restraints weight = 31158.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065182 restraints weight = 19711.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.066111 restraints weight = 14351.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066735 restraints weight = 11430.032| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 24651 Z= 0.295 Angle : 0.661 10.026 33427 Z= 0.346 Chirality : 0.049 0.158 3852 Planarity : 0.005 0.065 4362 Dihedral : 5.974 88.012 3422 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.01 % Allowed : 8.45 % Favored : 90.54 % 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: 0.46 (0.15), residues: 3115 helix: 1.18 (0.15), residues: 1231 sheet: 0.23 (0.21), residues: 556 loop : -0.41 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 164 TYR 0.019 0.002 TYR G 78 PHE 0.017 0.002 PHE A 494 HIS 0.006 0.002 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.30 (24651) covalent geometry : angle 0.66059 / 0.35 (33427) hydrogen bonds : bond 0.05646 / 3.82 ( 1165) hydrogen bonds : angle 5.26061 / 3.79 ( 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: 26 poor density : 134 time to evaluate : 1.008 Fit side-chains REVERT: C 210 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: D 56 ASP cc_start: 0.7281 (t0) cc_final: 0.6746 (t0) REVERT: F 74 MET cc_start: 0.8833 (mtt) cc_final: 0.8617 (mtt) REVERT: F 170 GLU cc_start: 0.8254 (tp30) cc_final: 0.7700 (tp30) REVERT: F 213 MET cc_start: 0.8380 (mtp) cc_final: 0.7957 (mtm) REVERT: G 106 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6682 (ttm110) REVERT: G 241 MET cc_start: 0.6712 (ttt) cc_final: 0.6423 (ttt) outliers start: 26 outliers final: 12 residues processed: 152 average time/residue: 0.1571 time to fit residues: 39.7423 Evaluate side-chains 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 366 VAL 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: 0.9990 chunk 249 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 182 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3176 r_free = 0.3176 target = 0.080121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.063636 restraints weight = 60528.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065773 restraints weight = 30747.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.067183 restraints weight = 19363.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068119 restraints weight = 14019.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068711 restraints weight = 11179.596| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24651 Z= 0.136 Angle : 0.528 9.382 33427 Z= 0.276 Chirality : 0.044 0.163 3852 Planarity : 0.004 0.058 4362 Dihedral : 5.603 87.814 3422 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.21 % Allowed : 9.31 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1232 sheet: 0.36 (0.21), residues: 545 loop : -0.33 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.015 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/Z covalent geometry : bond 0.00318 / 0.14 (24651) covalent geometry : angle 0.52805 / 0.28 (33427) hydrogen bonds : bond 0.04396 / 2.99 ( 1165) hydrogen bonds : angle 4.89643 / 3.53 ( 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 167 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.017 Fit side-chains REVERT: A 397 GLN cc_start: 0.4491 (OUTLIER) cc_final: 0.3656 (pm20) REVERT: D 56 ASP cc_start: 0.7228 (t0) cc_final: 0.6663 (t0) REVERT: D 74 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8699 (mtt) REVERT: F 74 MET cc_start: 0.8789 (mtt) cc_final: 0.8581 (mtt) REVERT: F 170 GLU cc_start: 0.8194 (tp30) cc_final: 0.7673 (tp30) REVERT: F 213 MET cc_start: 0.8368 (mtp) cc_final: 0.7921 (mtm) outliers start: 31 outliers final: 17 residues processed: 160 average time/residue: 0.1507 time to fit residues: 40.8910 Evaluate side-chains 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 314 THR Chi-restraints excluded: chain D residue 74 MET 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 E residue 90 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 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: 0.8980 chunk 299 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3193 r_free = 0.3193 target = 0.081018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064619 restraints weight = 60192.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.066762 restraints weight = 30328.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068172 restraints weight = 19000.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069109 restraints weight = 13731.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069732 restraints weight = 10925.529| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24651 Z= 0.110 Angle : 0.501 8.757 33427 Z= 0.260 Chirality : 0.043 0.152 3852 Planarity : 0.004 0.054 4362 Dihedral : 5.378 87.060 3422 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.32 % Allowed : 9.89 % Favored : 88.79 % 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: 0.96 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1235 sheet: 0.44 (0.22), residues: 552 loop : -0.25 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 140 TYR 0.013 0.001 TYR G 78 PHE 0.010 0.001 PHE G 205 HIS 0.004 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (24651) covalent geometry : angle 0.50058 / 0.26 (33427) hydrogen bonds : bond 0.03983 / 2.72 ( 1165) hydrogen bonds : angle 4.72436 / 3.41 ( 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 174 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.910 Fit side-chains REVERT: A 397 GLN cc_start: 0.4412 (OUTLIER) cc_final: 0.3597 (pm20) REVERT: C 210 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 56 ASP cc_start: 0.7216 (t0) cc_final: 0.6645 (t0) REVERT: D 74 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8663 (mtt) REVERT: F 170 GLU cc_start: 0.8179 (tp30) cc_final: 0.7587 (tp30) REVERT: F 213 MET cc_start: 0.8385 (mtp) cc_final: 0.8157 (mtt) REVERT: G 216 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6257 (tp) REVERT: G 241 MET cc_start: 0.6728 (ttt) cc_final: 0.6281 (ttt) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 0.1534 time to fit residues: 43.4138 Evaluate side-chains 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 314 THR 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 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 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 420 PHE 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 73 VAL Chi-restraints excluded: chain G residue 216 LEU 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: 0.0020 chunk 298 optimal weight: 20.0000 chunk 260 optimal weight: 6.9990 chunk 100 optimal weight: 0.0020 chunk 97 optimal weight: 0.3980 chunk 280 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 136 optimal weight: 0.0970 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3205 r_free = 0.3205 target = 0.081576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.065199 restraints weight = 59947.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.067338 restraints weight = 30134.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068748 restraints weight = 18855.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.069663 restraints weight = 13583.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070303 restraints weight = 10829.280| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24651 Z= 0.098 Angle : 0.487 8.228 33427 Z= 0.252 Chirality : 0.043 0.222 3852 Planarity : 0.004 0.050 4362 Dihedral : 5.216 88.394 3422 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.60 % Allowed : 10.09 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3115 helix: 1.84 (0.15), residues: 1236 sheet: 0.53 (0.22), residues: 555 loop : -0.15 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 3 TYR 0.013 0.001 TYR B 389 PHE 0.008 0.001 PHE B 456 HIS 0.004 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (24651) covalent geometry : angle 0.48708 / 0.25 (33427) hydrogen bonds : bond 0.03739 / 2.56 ( 1165) hydrogen bonds : angle 4.62112 / 3.33 ( 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 182 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 1.063 Fit side-chains REVERT: A 397 GLN cc_start: 0.4348 (OUTLIER) cc_final: 0.3560 (pm20) REVERT: B 272 GLU cc_start: 0.7957 (tt0) cc_final: 0.7686 (tt0) REVERT: C 210 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: D 56 ASP cc_start: 0.7225 (t0) cc_final: 0.6598 (t0) REVERT: D 74 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8643 (mtt) REVERT: E 275 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8783 (t) REVERT: F 1 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5505 (tpp) REVERT: F 74 MET cc_start: 0.8806 (mtt) cc_final: 0.8437 (mtt) REVERT: F 170 GLU cc_start: 0.8167 (tp30) cc_final: 0.7570 (tp30) REVERT: G 216 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6253 (tp) outliers start: 41 outliers final: 22 residues processed: 173 average time/residue: 0.1513 time to fit residues: 44.6769 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 314 THR 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 253 ASN 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 E residue 344 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 305 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 chunk 309 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN C 189 GLN D 253 ASN ** G 65 HIS ** 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 = 0.3139 r_free = 0.3139 target = 0.078199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061857 restraints weight = 60916.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063910 restraints weight = 31181.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.065290 restraints weight = 19767.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.066194 restraints weight = 14372.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.066794 restraints weight = 11486.816| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 24651 Z= 0.280 Angle : 0.641 10.061 33427 Z= 0.333 Chirality : 0.048 0.169 3852 Planarity : 0.005 0.064 4362 Dihedral : 5.746 89.106 3422 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 10.63 % Favored : 87.69 % 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: 0.63 (0.15), residues: 3115 helix: 1.38 (0.15), residues: 1233 sheet: 0.40 (0.22), residues: 539 loop : -0.40 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 333 TYR 0.018 0.002 TYR G 78 PHE 0.018 0.002 PHE A 494 HIS 0.006 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.28 (24651) covalent geometry : angle 0.64138 / 0.33 (33427) hydrogen bonds : bond 0.05327 / 3.60 ( 1165) hydrogen bonds : angle 5.02209 / 3.62 ( 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 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.053 Fit side-chains REVERT: A 397 GLN cc_start: 0.4533 (OUTLIER) cc_final: 0.3773 (pm20) REVERT: C 210 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 407 GLN cc_start: 0.6806 (pm20) cc_final: 0.6481 (mp10) REVERT: D 56 ASP cc_start: 0.7369 (t0) cc_final: 0.6752 (t0) REVERT: D 74 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: D 253 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (m110) REVERT: D 271 MET cc_start: 0.8727 (mmm) cc_final: 0.8265 (mtt) REVERT: E 275 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8821 (t) REVERT: F 1 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.5536 (tpp) REVERT: F 74 MET cc_start: 0.8871 (mtt) cc_final: 0.8569 (mtt) REVERT: F 170 GLU cc_start: 0.8247 (tp30) cc_final: 0.7640 (tp30) REVERT: G 216 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6329 (tp) outliers start: 43 outliers final: 28 residues processed: 162 average time/residue: 0.1555 time to fit residues: 42.3778 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 A residue 397 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 430 VAL 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 210 GLU Chi-restraints excluded: chain C residue 243 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 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 275 VAL 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 1 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 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 Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 253 ASN F 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 = 0.3192 r_free = 0.3192 target = 0.080832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.064980 restraints weight = 59747.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.066995 restraints weight = 31032.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068352 restraints weight = 19749.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069237 restraints weight = 14329.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069830 restraints weight = 11508.316| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24651 Z= 0.114 Angle : 0.514 8.818 33427 Z= 0.265 Chirality : 0.044 0.194 3852 Planarity : 0.004 0.056 4362 Dihedral : 5.440 89.703 3422 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.48 % Allowed : 10.98 % Favored : 87.54 % 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: 0.96 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1233 sheet: 0.50 (0.22), residues: 544 loop : -0.26 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 405 TYR 0.014 0.001 TYR B 389 PHE 0.015 0.001 PHE A 395 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (24651) covalent geometry : angle 0.51356 / 0.26 (33427) hydrogen bonds : bond 0.04083 / 2.78 ( 1165) hydrogen bonds : angle 4.72158 / 3.41 ( 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 166 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.044 Fit side-chains REVERT: A 397 GLN cc_start: 0.4535 (OUTLIER) cc_final: 0.3766 (pm20) REVERT: C 210 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 56 ASP cc_start: 0.7224 (t0) cc_final: 0.6646 (t0) REVERT: D 74 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8657 (mtt) REVERT: E 275 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8782 (t) REVERT: F 1 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5459 (tpp) REVERT: F 74 MET cc_start: 0.8825 (mtt) cc_final: 0.8528 (mtt) REVERT: F 170 GLU cc_start: 0.8109 (tp30) cc_final: 0.7624 (tp30) REVERT: G 216 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6391 (tp) outliers start: 38 outliers final: 25 residues processed: 160 average time/residue: 0.1520 time to fit residues: 41.4577 Evaluate side-chains 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 B residue 500 VAL 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 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 275 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain F residue 1 MET 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 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: 1.9990 chunk 277 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 295 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 GLN ** 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 = 0.3163 r_free = 0.3163 target = 0.079413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063122 restraints weight = 60499.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.065222 restraints weight = 30622.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.066597 restraints weight = 19225.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067502 restraints weight = 13901.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068104 restraints weight = 11092.375| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24651 Z= 0.194 Angle : 0.560 8.911 33427 Z= 0.289 Chirality : 0.046 0.153 3852 Planarity : 0.004 0.058 4362 Dihedral : 5.502 88.485 3422 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.60 % Allowed : 11.33 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1234 sheet: 0.52 (0.22), residues: 527 loop : -0.35 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 106 TYR 0.015 0.001 TYR B 389 PHE 0.013 0.001 PHE A 494 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (24651) covalent geometry : angle 0.55980 / 0.29 (33427) hydrogen bonds : bond 0.04579 / 3.11 ( 1165) hydrogen bonds : angle 4.80785 / 3.47 ( 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 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.993 Fit side-chains REVERT: A 250 MET cc_start: 0.8456 (tpp) cc_final: 0.8051 (ttm) REVERT: A 397 GLN cc_start: 0.4475 (OUTLIER) cc_final: 0.3696 (pm20) REVERT: C 210 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: D 56 ASP cc_start: 0.7390 (t0) cc_final: 0.6780 (t0) REVERT: D 74 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8657 (mtt) REVERT: E 275 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8783 (t) REVERT: F 1 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5467 (tpp) REVERT: F 74 MET cc_start: 0.8853 (mtt) cc_final: 0.8550 (mtt) REVERT: F 170 GLU cc_start: 0.8226 (tp30) cc_final: 0.7643 (tp30) REVERT: G 216 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6323 (tp) outliers start: 41 outliers final: 30 residues processed: 158 average time/residue: 0.1473 time to fit residues: 40.1600 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 B residue 500 VAL 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 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 275 VAL 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 1 MET Chi-restraints excluded: chain F residue 87 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 226 optimal weight: 0.0030 chunk 207 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3164 r_free = 0.3164 target = 0.079507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.063165 restraints weight = 60369.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.065253 restraints weight = 30650.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.066632 restraints weight = 19289.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067543 restraints weight = 13993.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068102 restraints weight = 11179.417| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24651 Z= 0.184 Angle : 0.557 8.849 33427 Z= 0.288 Chirality : 0.046 0.251 3852 Planarity : 0.004 0.058 4362 Dihedral : 5.509 88.522 3422 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.40 % Allowed : 11.45 % Favored : 87.15 % 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: 0.81 (0.15), residues: 3115 helix: 1.59 (0.15), residues: 1233 sheet: 0.47 (0.22), residues: 523 loop : -0.36 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 333 TYR 0.015 0.001 TYR B 389 PHE 0.018 0.001 PHE A 395 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (24651) covalent geometry : angle 0.55652 / 0.29 (33427) hydrogen bonds : bond 0.04555 / 3.09 ( 1165) hydrogen bonds : angle 4.81722 / 3.49 ( 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 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.041 Fit side-chains REVERT: A 250 MET cc_start: 0.8436 (tpp) cc_final: 0.8034 (ttm) REVERT: A 397 GLN cc_start: 0.4502 (OUTLIER) cc_final: 0.3700 (pm20) REVERT: C 210 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 56 ASP cc_start: 0.7425 (t0) cc_final: 0.6786 (t0) REVERT: D 74 MET cc_start: 0.8909 (ttm) cc_final: 0.8635 (mtt) REVERT: E 275 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8744 (t) REVERT: F 1 MET cc_start: 0.6070 (OUTLIER) cc_final: 0.5425 (tpp) REVERT: F 74 MET cc_start: 0.8848 (mtt) cc_final: 0.8545 (mtt) REVERT: F 170 GLU cc_start: 0.8225 (tp30) cc_final: 0.7644 (tp30) REVERT: G 216 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6330 (tp) REVERT: G 241 MET cc_start: 0.6469 (ttt) cc_final: 0.6173 (tpp) outliers start: 36 outliers final: 31 residues processed: 155 average time/residue: 0.1487 time to fit residues: 39.6745 Evaluate side-chains 159 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 B residue 500 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 202 MET 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 275 VAL 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 1 MET Chi-restraints excluded: chain F residue 87 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 136 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 258 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 203 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 253 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 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 = 0.3213 r_free = 0.3213 target = 0.081859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.065923 restraints weight = 59679.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.067971 restraints weight = 31043.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069324 restraints weight = 19687.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070221 restraints weight = 14318.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.070794 restraints weight = 11478.794| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24651 Z= 0.102 Angle : 0.494 8.876 33427 Z= 0.254 Chirality : 0.043 0.158 3852 Planarity : 0.004 0.051 4362 Dihedral : 5.205 89.127 3422 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 11.92 % Favored : 86.92 % 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: 1.86 (0.15), residues: 1235 sheet: 0.66 (0.22), residues: 535 loop : -0.20 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 405 TYR 0.013 0.001 TYR B 389 PHE 0.010 0.001 PHE C 395 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (24651) covalent geometry : angle 0.49417 / 0.25 (33427) hydrogen bonds : bond 0.03661 / 2.51 ( 1165) hydrogen bonds : angle 4.58581 / 3.32 ( 3336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3448.06 seconds wall clock time: 60 minutes 50.84 seconds (3650.84 seconds total)