Starting phenix.real_space_refine on Sat Jun 21 04:16:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hhb_34758/06_2025/8hhb_34758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hhb_34758/06_2025/8hhb_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_34758/06_2025/8hhb_34758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hhb_34758/06_2025/8hhb_34758.map" model { file = "/net/cci-nas-00/data/ceres_data/8hhb_34758/06_2025/8hhb_34758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hhb_34758/06_2025/8hhb_34758.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.71, per 1000 atoms: 0.61 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: 5.70 Conformation dependent library (CDL) restraints added in 3.3 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 21 sheets defined 48.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 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: 10.02 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8232 1.34 - 1.46: 4728 1.46 - 1.58: 11523 1.58 - 1.70: 14 1.70 - 1.82: 154 Bond restraints: 24651 Sorted by residual: bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.505 0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" C HIS G 65 " pdb=" N PRO G 66 " ideal model delta sigma weight residual 1.332 1.350 -0.017 8.90e-03 1.26e+04 3.71e+00 ... (remaining 24646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 32633 1.74 - 3.48: 698 3.48 - 5.21: 83 5.21 - 6.95: 10 6.95 - 8.69: 3 Bond angle restraints: 33427 Sorted by residual: angle pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" C VAL A 25 " ideal model delta sigma weight residual 113.20 108.54 4.66 9.60e-01 1.09e+00 2.35e+01 angle pdb=" CA GLY F 298 " pdb=" C GLY F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 114.58 117.48 -2.90 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N VAL D 275 " pdb=" CA VAL D 275 " pdb=" C VAL D 275 " ideal model delta sigma weight residual 111.77 108.31 3.46 1.04e+00 9.25e-01 1.11e+01 angle pdb=" C GLY D 443 " pdb=" N LYS D 444 " pdb=" CA LYS D 444 " ideal model delta sigma weight residual 122.55 115.83 6.72 2.03e+00 2.43e-01 1.09e+01 angle pdb=" N ASP B 262 " pdb=" CA ASP B 262 " pdb=" C ASP B 262 " ideal model delta sigma weight residual 107.32 112.58 -5.26 1.65e+00 3.67e-01 1.02e+01 ... (remaining 33422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.25: 14066 21.25 - 42.50: 811 42.50 - 63.74: 125 63.74 - 84.99: 45 84.99 - 106.24: 12 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PB ADP D 603 " pdb=" PA ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 -166.24 106.24 1 2.00e+01 2.50e-03 3.07e+01 dihedral pdb=" CA GLU G 204 " pdb=" C GLU G 204 " pdb=" N PHE G 205 " pdb=" CA PHE G 205 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TYR G 203 " pdb=" C TYR G 203 " pdb=" N GLU G 204 " pdb=" CA GLU G 204 " ideal model delta harmonic sigma weight residual 180.00 158.34 21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2613 0.041 - 0.082: 873 0.082 - 0.123: 332 0.123 - 0.165: 32 0.165 - 0.206: 2 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA PRO B 482 " pdb=" N PRO B 482 " pdb=" C PRO B 482 " pdb=" CB PRO B 482 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL D 87 " pdb=" CA VAL D 87 " pdb=" CG1 VAL D 87 " pdb=" CG2 VAL D 87 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA LEU G 189 " pdb=" N LEU G 189 " pdb=" C LEU G 189 " pdb=" CB LEU G 189 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 109 " -0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO G 110 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO G 110 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 110 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 481 " -0.063 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO B 482 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 482 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 482 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 409 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C LYS B 409 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS B 409 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 410 " 0.011 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 103 2.51 - 3.10: 17926 3.10 - 3.70: 36317 3.70 - 4.30: 52115 4.30 - 4.90: 89705 Nonbonded interactions: 196166 Sorted by model distance: nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.908 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.912 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 602 " model vdw 1.953 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 1.962 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2B ATP C 602 " model vdw 2.004 2.170 ... (remaining 196161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = chain 'E' selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 56.280 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24651 Z= 0.190 Angle : 0.628 8.689 33427 Z= 0.356 Chirality : 0.046 0.206 3852 Planarity : 0.005 0.094 4362 Dihedral : 14.333 106.240 9347 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (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 HIS 0.005 0.001 HIS E 401 PHE 0.030 0.001 PHE G 205 TYR 0.019 0.002 TYR C 329 ARG 0.007 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.14896 ( 1165) hydrogen bonds : angle 6.30377 ( 3336) covalent geometry : bond 0.00431 (24651) covalent geometry : angle 0.62782 (33427) *********************** 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 : 2.593 Fit side-chains REVERT: B 272 GLU cc_start: 0.7994 (tt0) cc_final: 0.7705 (tp30) REVERT: D 56 ASP cc_start: 0.7183 (t0) cc_final: 0.6742 (t0) REVERT: F 74 MET cc_start: 0.8794 (mtt) cc_final: 0.8545 (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: 0.3405 time to fit residues: 90.4240 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 : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 GLN D 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.063588 restraints weight = 60326.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.065712 restraints weight = 30671.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067113 restraints weight = 19328.271| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24651 Z= 0.191 Angle : 0.579 8.104 33427 Z= 0.305 Chirality : 0.046 0.183 3852 Planarity : 0.005 0.066 4362 Dihedral : 7.853 87.851 3546 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.31 % Allowed : 5.06 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3115 helix: 1.49 (0.15), residues: 1238 sheet: 0.57 (0.22), residues: 556 loop : -0.16 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.015 0.001 PHE G 205 TYR 0.015 0.001 TYR C 329 ARG 0.005 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 1165) hydrogen bonds : angle 5.19021 ( 3336) covalent geometry : bond 0.00456 (24651) covalent geometry : angle 0.57866 (33427) *********************** 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 148 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 2.608 Fit side-chains REVERT: B 48 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8669 (ptp) REVERT: D 56 ASP cc_start: 0.7250 (t0) cc_final: 0.6692 (t0) REVERT: F 170 GLU cc_start: 0.8274 (tp30) cc_final: 0.7853 (tp30) outliers start: 8 outliers final: 6 residues processed: 146 average time/residue: 0.3277 time to fit residues: 79.7379 Evaluate side-chains 135 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 267 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN D 381 GLN ** 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 = 0.3191 r_free = 0.3191 target = 0.080934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.064491 restraints weight = 59679.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.066619 restraints weight = 30170.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068026 restraints weight = 18994.528| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24651 Z= 0.133 Angle : 0.520 9.001 33427 Z= 0.272 Chirality : 0.044 0.147 3852 Planarity : 0.004 0.059 4362 Dihedral : 7.318 80.799 3546 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.74 % Allowed : 6.58 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1242 sheet: 0.56 (0.21), residues: 557 loop : -0.15 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.014 0.001 PHE G 205 TYR 0.013 0.001 TYR C 329 ARG 0.004 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 1165) hydrogen bonds : angle 4.87584 ( 3336) covalent geometry : bond 0.00308 (24651) covalent geometry : angle 0.51992 (33427) *********************** 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 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 2.770 Fit side-chains REVERT: D 56 ASP cc_start: 0.7232 (t0) cc_final: 0.6642 (t0) REVERT: D 74 MET cc_start: 0.9026 (ttm) cc_final: 0.8746 (mtt) REVERT: F 170 GLU cc_start: 0.8207 (tp30) cc_final: 0.7700 (tp30) outliers start: 19 outliers final: 10 residues processed: 153 average time/residue: 0.3304 time to fit residues: 85.9254 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 475 ILE 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 F residue 87 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 254 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN C 474 HIS ** 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 = 0.3143 r_free = 0.3143 target = 0.078449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.062035 restraints weight = 61064.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.064105 restraints weight = 31102.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.065473 restraints weight = 19666.493| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 24651 Z= 0.278 Angle : 0.634 9.729 33427 Z= 0.331 Chirality : 0.048 0.155 3852 Planarity : 0.005 0.065 4362 Dihedral : 7.547 82.643 3546 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.36 % Allowed : 8.72 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3115 helix: 1.35 (0.15), residues: 1231 sheet: 0.31 (0.21), residues: 546 loop : -0.37 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 401 PHE 0.016 0.002 PHE A 494 TYR 0.018 0.002 TYR G 78 ARG 0.004 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 1165) hydrogen bonds : angle 5.08259 ( 3336) covalent geometry : bond 0.00670 (24651) covalent geometry : angle 0.63430 (33427) *********************** 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 169 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 2.830 Fit side-chains REVERT: A 397 GLN cc_start: 0.4424 (OUTLIER) cc_final: 0.3625 (pm20) REVERT: D 56 ASP cc_start: 0.7340 (t0) cc_final: 0.6770 (t0) REVERT: D 74 MET cc_start: 0.9059 (ttm) cc_final: 0.8755 (mtt) REVERT: F 74 MET cc_start: 0.9012 (mtt) cc_final: 0.8653 (mtt) REVERT: F 170 GLU cc_start: 0.8201 (tp30) cc_final: 0.7647 (tp30) REVERT: G 276 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7925 (tt0) outliers start: 35 outliers final: 18 residues processed: 161 average time/residue: 0.3313 time to fit residues: 88.9494 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 : 2.783 ------------------------------------------------------------------------------- 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 A residue 397 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 43 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 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 139 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.063201 restraints weight = 60684.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065316 restraints weight = 30794.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.066701 restraints weight = 19380.629| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24651 Z= 0.166 Angle : 0.542 9.081 33427 Z= 0.284 Chirality : 0.045 0.158 3852 Planarity : 0.004 0.061 4362 Dihedral : 7.354 88.685 3546 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.25 % Allowed : 9.85 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1234 sheet: 0.37 (0.22), residues: 544 loop : -0.35 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.011 0.001 PHE A 494 TYR 0.015 0.001 TYR G 78 ARG 0.004 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 1165) hydrogen bonds : angle 4.88809 ( 3336) covalent geometry : bond 0.00395 (24651) covalent geometry : angle 0.54235 (33427) *********************** 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 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 2.936 Fit side-chains REVERT: A 397 GLN cc_start: 0.4429 (OUTLIER) cc_final: 0.3646 (pm20) REVERT: D 56 ASP cc_start: 0.7300 (t0) cc_final: 0.6723 (t0) REVERT: D 74 MET cc_start: 0.9015 (ttm) cc_final: 0.8736 (mtt) REVERT: F 74 MET cc_start: 0.8986 (mtt) cc_final: 0.8579 (mtt) REVERT: F 170 GLU cc_start: 0.8184 (tp30) cc_final: 0.7595 (tp30) REVERT: G 216 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6302 (tp) outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.3867 time to fit residues: 103.2100 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 4.230 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain 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 170 MET 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 136 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 219 optimal weight: 0.0770 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.064821 restraints weight = 59976.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066966 restraints weight = 30238.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068371 restraints weight = 18925.410| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24651 Z= 0.104 Angle : 0.494 8.516 33427 Z= 0.257 Chirality : 0.043 0.237 3852 Planarity : 0.004 0.054 4362 Dihedral : 7.034 84.268 3546 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.25 % Allowed : 10.24 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1235 sheet: 0.50 (0.22), residues: 552 loop : -0.22 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.010 0.001 PHE B 456 TYR 0.011 0.001 TYR G 78 ARG 0.003 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 1165) hydrogen bonds : angle 4.67513 ( 3336) covalent geometry : bond 0.00225 (24651) covalent geometry : angle 0.49389 (33427) *********************** 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 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 2.715 Fit side-chains REVERT: B 272 GLU cc_start: 0.7996 (tt0) cc_final: 0.7753 (tt0) REVERT: D 56 ASP cc_start: 0.7331 (t0) cc_final: 0.6673 (t0) REVERT: D 74 MET cc_start: 0.8975 (ttm) cc_final: 0.8687 (mtt) REVERT: E 275 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8795 (t) REVERT: F 74 MET cc_start: 0.8955 (mtt) cc_final: 0.8567 (mtt) REVERT: F 170 GLU cc_start: 0.8166 (tp30) cc_final: 0.7581 (tp30) outliers start: 32 outliers final: 22 residues processed: 167 average time/residue: 0.3786 time to fit residues: 107.6814 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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 B residue 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 170 MET 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 221 optimal weight: 0.0970 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 134 optimal weight: 0.0970 chunk 17 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.063011 restraints weight = 60809.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065105 restraints weight = 30909.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.066489 restraints weight = 19508.389| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24651 Z= 0.204 Angle : 0.564 8.958 33427 Z= 0.293 Chirality : 0.046 0.155 3852 Planarity : 0.004 0.060 4362 Dihedral : 7.100 82.546 3546 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.60 % Allowed : 10.48 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1232 sheet: 0.46 (0.22), residues: 540 loop : -0.31 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.014 0.001 PHE A 494 TYR 0.015 0.001 TYR G 78 ARG 0.004 0.000 ARG E 458 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 1165) hydrogen bonds : angle 4.81999 ( 3336) covalent geometry : bond 0.00491 (24651) covalent geometry : angle 0.56352 (33427) *********************** 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 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 2.959 Fit side-chains REVERT: A 397 GLN cc_start: 0.4445 (OUTLIER) cc_final: 0.3679 (pm20) REVERT: D 56 ASP cc_start: 0.7412 (t0) cc_final: 0.6766 (t0) REVERT: D 74 MET cc_start: 0.9008 (ttm) cc_final: 0.8731 (mtt) REVERT: E 218 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8119 (mtt) REVERT: E 275 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8816 (t) REVERT: F 74 MET cc_start: 0.8963 (mtt) cc_final: 0.8609 (mtt) REVERT: F 170 GLU cc_start: 0.8221 (tp30) cc_final: 0.7600 (tp30) REVERT: G 216 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6303 (tp) outliers start: 41 outliers final: 31 residues processed: 166 average time/residue: 0.3150 time to fit residues: 89.4977 Evaluate side-chains 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 MET Chi-restraints excluded: chain B residue 173 THR 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 243 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 340 ILE 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 218 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 170 MET 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 9 optimal weight: 7.9990 chunk 243 optimal weight: 0.7980 chunk 208 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.063352 restraints weight = 60459.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.065451 restraints weight = 30699.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066872 restraints weight = 19355.263| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24651 Z= 0.172 Angle : 0.546 8.763 33427 Z= 0.283 Chirality : 0.045 0.205 3852 Planarity : 0.004 0.059 4362 Dihedral : 7.051 83.773 3546 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.64 % Allowed : 11.06 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3115 helix: 1.61 (0.15), residues: 1234 sheet: 0.51 (0.22), residues: 527 loop : -0.33 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.011 0.001 PHE A 494 TYR 0.014 0.001 TYR G 78 ARG 0.002 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1165) hydrogen bonds : angle 4.78935 ( 3336) covalent geometry : bond 0.00409 (24651) covalent geometry : angle 0.54572 (33427) *********************** 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 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 2.782 Fit side-chains REVERT: A 397 GLN cc_start: 0.4430 (OUTLIER) cc_final: 0.3650 (pm20) REVERT: D 56 ASP cc_start: 0.7412 (t0) cc_final: 0.6768 (t0) REVERT: D 74 MET cc_start: 0.9006 (ttm) cc_final: 0.8752 (mtt) REVERT: E 275 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8787 (t) REVERT: F 1 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5525 (tpp) REVERT: F 74 MET cc_start: 0.8952 (mtt) cc_final: 0.8584 (mtt) REVERT: F 170 GLU cc_start: 0.8216 (tp30) cc_final: 0.7616 (tp30) REVERT: G 216 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6341 (tp) outliers start: 42 outliers final: 33 residues processed: 161 average time/residue: 0.3167 time to fit residues: 87.6511 Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 340 ILE 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 421 THR 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 170 MET 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 90 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 182 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 288 optimal weight: 0.6980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.079470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.063072 restraints weight = 60598.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.065162 restraints weight = 30782.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066539 restraints weight = 19407.344| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24651 Z= 0.191 Angle : 0.564 9.026 33427 Z= 0.292 Chirality : 0.046 0.154 3852 Planarity : 0.004 0.060 4362 Dihedral : 7.064 86.782 3546 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.52 % Allowed : 11.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1235 sheet: 0.46 (0.22), residues: 527 loop : -0.38 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.016 0.001 PHE A 395 TYR 0.014 0.001 TYR G 78 ARG 0.002 0.000 ARG F 3 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 1165) hydrogen bonds : angle 4.84041 ( 3336) covalent geometry : bond 0.00457 (24651) covalent geometry : angle 0.56365 (33427) *********************** 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 162 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 2.625 Fit side-chains REVERT: A 397 GLN cc_start: 0.4564 (OUTLIER) cc_final: 0.3795 (pm20) REVERT: D 56 ASP cc_start: 0.7420 (t0) cc_final: 0.6808 (t0) REVERT: D 74 MET cc_start: 0.9013 (ttm) cc_final: 0.8761 (mtt) REVERT: E 275 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8809 (t) REVERT: F 1 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5459 (tpp) REVERT: F 74 MET cc_start: 0.8946 (mtt) cc_final: 0.8623 (mtt) REVERT: F 170 GLU cc_start: 0.8190 (tp30) cc_final: 0.7674 (tp30) REVERT: G 216 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6349 (tp) outliers start: 39 outliers final: 33 residues processed: 156 average time/residue: 0.3531 time to fit residues: 93.0877 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 340 ILE 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 421 THR 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 170 MET 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 250 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 278 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.063744 restraints weight = 60292.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065835 restraints weight = 30479.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.067253 restraints weight = 19162.491| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24651 Z= 0.148 Angle : 0.534 8.801 33427 Z= 0.277 Chirality : 0.045 0.262 3852 Planarity : 0.004 0.058 4362 Dihedral : 6.924 89.493 3546 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.52 % Allowed : 11.37 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3115 helix: 1.64 (0.15), residues: 1235 sheet: 0.50 (0.22), residues: 521 loop : -0.32 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 363 PHE 0.011 0.001 PHE F 257 TYR 0.013 0.001 TYR G 78 ARG 0.003 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 1165) hydrogen bonds : angle 4.76262 ( 3336) covalent geometry : bond 0.00347 (24651) covalent geometry : angle 0.53449 (33427) ********************** 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 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 2.802 Fit side-chains REVERT: A 250 MET cc_start: 0.8448 (tpp) cc_final: 0.7894 (ttm) REVERT: A 397 GLN cc_start: 0.4460 (OUTLIER) cc_final: 0.3669 (pm20) REVERT: D 56 ASP cc_start: 0.7436 (t0) cc_final: 0.6791 (t0) REVERT: D 74 MET cc_start: 0.8982 (ttm) cc_final: 0.8732 (mtt) REVERT: E 275 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8767 (t) REVERT: F 1 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5412 (tpp) REVERT: F 74 MET cc_start: 0.8954 (mtt) cc_final: 0.8586 (mtt) REVERT: F 170 GLU cc_start: 0.8185 (tp30) cc_final: 0.7603 (tp30) REVERT: G 216 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6338 (tp) REVERT: G 241 MET cc_start: 0.7068 (tpp) cc_final: 0.6820 (mmm) outliers start: 39 outliers final: 32 residues processed: 158 average time/residue: 0.3151 time to fit residues: 86.3433 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 MET Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 115 VAL 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 252 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 340 ILE 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 66 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 176 optimal weight: 0.0040 chunk 132 optimal weight: 5.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3166 r_free = 0.3166 target = 0.079652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.063256 restraints weight = 60579.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065351 restraints weight = 30777.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066739 restraints weight = 19366.276| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24651 Z= 0.176 Angle : 0.551 9.000 33427 Z= 0.286 Chirality : 0.045 0.210 3852 Planarity : 0.004 0.059 4362 Dihedral : 6.910 88.550 3546 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.52 % Allowed : 11.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3115 helix: 1.58 (0.15), residues: 1235 sheet: 0.46 (0.22), residues: 521 loop : -0.35 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.017 0.001 PHE A 395 TYR 0.014 0.001 TYR G 78 ARG 0.003 0.000 ARG E 3 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1165) hydrogen bonds : angle 4.80373 ( 3336) covalent geometry : bond 0.00421 (24651) covalent geometry : angle 0.55059 (33427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6523.16 seconds wall clock time: 119 minutes 4.20 seconds (7144.20 seconds total)