Starting phenix.real_space_refine on Fri Jul 3 20:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpo_22417/07_2026/7jpo_22417_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10306 2.51 5 N 2724 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16087 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4863 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 24, 'TRANS': 569} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3301 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 19, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "D" 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: "E" 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: 3.19, per 1000 atoms: 0.20 Number of scatterers: 16087 At special positions: 0 Unit cell: (90.95, 133.75, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 9 15.00 Mg 3 11.99 O 2962 8.00 N 2724 7.00 C 10306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 741.3 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 62.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.659A pdb=" N PHE A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 577 through 588 removed outlier: 4.230A pdb=" N VAL A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.874A pdb=" N LEU A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 626 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 4.183A pdb=" N TYR A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 removed outlier: 4.195A pdb=" N GLU A 660 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.505A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 Processing helix chain 'A' and resid 718 through 736 removed outlier: 3.984A pdb=" N CYS A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.563A pdb=" N SER A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 795 through 810 removed outlier: 3.952A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.934A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.937A pdb=" N ASN B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.679A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.705A pdb=" N HIS B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.942A pdb=" N TRP B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 66 removed outlier: 3.598A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 87 removed outlier: 3.509A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.834A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.742A pdb=" N ASP C 140 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 141 " --> pdb=" O ALA C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.579A pdb=" N SER C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.870A pdb=" N LEU C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.668A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.549A pdb=" N HIS C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 320 through 339 removed outlier: 3.614A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.763A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.612A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 removed outlier: 3.625A pdb=" N CYS C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.609A pdb=" N GLN C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.524A pdb=" N LEU C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 451 through 461 removed outlier: 3.942A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 3.521A pdb=" N TYR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.851A pdb=" N ALA C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 566 Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 579 Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.646A pdb=" N LEU C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 605 Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.711A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 660 Processing helix chain 'C' and resid 675 through 690 removed outlier: 3.854A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.965A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.523A pdb=" N ASN D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.813A pdb=" N GLY D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.717A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.540A pdb=" N LEU D 201 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.652A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.809A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.784A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.937A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.608A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.684A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.590A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 42 through 54 removed outlier: 3.547A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.515A pdb=" N LEU E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 111 removed outlier: 3.970A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 130 Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.795A pdb=" N TYR E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.594A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.605A pdb=" N VAL E 241 " --> pdb=" O CYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 268 Proline residue: E 259 - end of helix removed outlier: 3.500A pdb=" N MET E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.713A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.502A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 3.913A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 Processing sheet with id=AA2, first strand: chain 'A' and resid 793 through 794 Processing sheet with id=AA3, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.701A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.533A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 95 through 100 removed outlier: 6.711A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.171A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE E 33 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 158 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE E 35 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 393 through 395 809 hydrogen bonds defined for protein. 2376 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: 2.29 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4137 1.33 - 1.46: 3174 1.46 - 1.58: 8968 1.58 - 1.70: 15 1.70 - 1.82: 125 Bond restraints: 16419 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 ... (remaining 16414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 21979 4.11 - 8.21: 229 8.21 - 12.32: 16 12.32 - 16.43: 3 16.43 - 20.54: 3 Bond angle restraints: 22230 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 122.38 14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.11 13.72 1.00e+00 1.00e+00 1.88e+02 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8831 17.98 - 35.96: 920 35.96 - 53.94: 173 53.94 - 71.92: 48 71.92 - 89.90: 29 Dihedral angle restraints: 10001 sinusoidal: 4163 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG D 359 " pdb=" C ARG D 359 " pdb=" N LYS D 360 " pdb=" CA LYS D 360 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL D 364 " pdb=" C VAL D 364 " pdb=" N TYR D 365 " pdb=" CA TYR D 365 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2109 0.073 - 0.146: 369 0.146 - 0.219: 47 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE C 643 " pdb=" CA ILE C 643 " pdb=" CG1 ILE C 643 " pdb=" CG2 ILE C 643 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2535 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 639 " -0.046 2.00e-02 2.50e+03 4.75e-02 5.65e+01 pdb=" CG TRP A 639 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP A 639 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 639 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 639 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 639 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 639 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 239 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " 0.015 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP C 448 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.000 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.69: 190 2.69 - 3.30: 17147 3.30 - 3.91: 29885 3.91 - 4.53: 40412 4.53 - 5.14: 63760 Nonbonded interactions: 151394 Sorted by model distance: nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E 502 " model vdw 2.073 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.090 2.170 nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR A 541 " pdb="MG MG A 902 " model vdw 2.123 2.170 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.124 2.170 ... (remaining 151389 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.007 0.081 16419 Z= 0.338 Angle : 1.085 20.536 22230 Z= 0.643 Chirality : 0.059 0.365 2538 Planarity : 0.007 0.079 2798 Dihedral : 15.981 89.895 6179 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 1928 helix: -1.10 (0.13), residues: 1105 sheet: -0.33 (0.35), residues: 187 loop : -1.74 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG C 353 TYR 0.039 0.003 TYR C 609 PHE 0.046 0.004 PHE D 132 TRP 0.127 0.005 TRP A 639 HIS 0.019 0.002 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.34 (16419) covalent geometry : angle 1.08519 / 0.64 (22230) hydrogen bonds : bond 0.17876 / 12.19 ( 809) hydrogen bonds : angle 6.16719 / 4.38 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 786 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6896 (mpt-90) REVERT: B 418 ILE cc_start: 0.7203 (tt) cc_final: 0.6987 (mt) REVERT: C 705 ARG cc_start: 0.5936 (mmp80) cc_final: 0.5280 (mmp-170) REVERT: D 247 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6568 (tm-30) REVERT: E 133 MET cc_start: 0.8204 (mtp) cc_final: 0.7691 (mtt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1319 time to fit residues: 48.0521 Evaluate side-chains 180 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 HIS A 688 GLN C 335 HIS C 458 GLN D 46 HIS D 57 HIS D 362 HIS E 100 ASN E 195 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.116179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095028 restraints weight = 26792.204| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.97 r_work: 0.3251 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16419 Z= 0.139 Angle : 0.567 6.092 22230 Z= 0.300 Chirality : 0.040 0.175 2538 Planarity : 0.005 0.055 2798 Dihedral : 8.818 83.432 2208 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.72 % Allowed : 6.38 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.18), residues: 1928 helix: 0.31 (0.15), residues: 1124 sheet: -0.18 (0.35), residues: 188 loop : -1.45 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 353 TYR 0.016 0.002 TYR A 683 PHE 0.022 0.002 PHE B 441 TRP 0.054 0.002 TRP A 639 HIS 0.008 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16419) covalent geometry : angle 0.56677 / 0.30 (22230) hydrogen bonds : bond 0.05090 / 3.46 ( 809) hydrogen bonds : angle 4.22231 / 3.01 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.597 Fit side-chains REVERT: A 493 LEU cc_start: 0.7959 (mp) cc_final: 0.7706 (mp) REVERT: A 571 MET cc_start: 0.8593 (tpp) cc_final: 0.8267 (mmt) REVERT: A 688 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6705 (tt0) REVERT: A 733 CYS cc_start: 0.7674 (t) cc_final: 0.7227 (t) REVERT: A 808 MET cc_start: 0.7872 (mpp) cc_final: 0.7572 (mpp) REVERT: B 418 ILE cc_start: 0.7983 (tt) cc_final: 0.7478 (mt) REVERT: C 705 ARG cc_start: 0.6544 (mmp80) cc_final: 0.5708 (mmp-170) REVERT: D 113 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7194 (mm-30) REVERT: D 284 MET cc_start: 0.8551 (tpt) cc_final: 0.7889 (tpt) REVERT: E 133 MET cc_start: 0.8717 (mtp) cc_final: 0.8299 (mtt) REVERT: E 252 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7882 (mmmt) outliers start: 13 outliers final: 9 residues processed: 200 average time/residue: 0.1222 time to fit residues: 36.0093 Evaluate side-chains 179 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 17 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 162 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 160 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 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 = 0.3663 r_free = 0.3663 target = 0.114370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093291 restraints weight = 27082.834| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.96 r_work: 0.3208 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16419 Z= 0.154 Angle : 0.552 6.493 22230 Z= 0.287 Chirality : 0.041 0.169 2538 Planarity : 0.004 0.045 2798 Dihedral : 8.819 88.060 2208 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.89 % Allowed : 8.93 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1928 helix: 0.78 (0.15), residues: 1138 sheet: -0.06 (0.36), residues: 188 loop : -1.44 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 353 TYR 0.014 0.002 TYR B 454 PHE 0.022 0.002 PHE B 441 TRP 0.048 0.002 TRP A 639 HIS 0.008 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (16419) covalent geometry : angle 0.55231 / 0.29 (22230) hydrogen bonds : bond 0.04731 / 3.23 ( 809) hydrogen bonds : angle 3.98758 / 2.83 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.8009 (mp) cc_final: 0.7719 (mp) REVERT: A 688 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: A 733 CYS cc_start: 0.7729 (t) cc_final: 0.7248 (t) REVERT: B 418 ILE cc_start: 0.8029 (tt) cc_final: 0.7524 (mt) REVERT: C 462 MET cc_start: 0.8429 (mmt) cc_final: 0.8198 (mmm) REVERT: C 605 ASN cc_start: 0.8040 (m-40) cc_final: 0.7791 (t0) REVERT: C 705 ARG cc_start: 0.6514 (mmp80) cc_final: 0.5896 (mmp-170) REVERT: D 113 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7147 (mm-30) REVERT: D 197 ASP cc_start: 0.8802 (p0) cc_final: 0.8394 (p0) REVERT: D 284 MET cc_start: 0.8654 (tpt) cc_final: 0.8109 (tpt) REVERT: E 252 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7913 (mmmt) outliers start: 16 outliers final: 12 residues processed: 195 average time/residue: 0.1185 time to fit residues: 34.6601 Evaluate side-chains 183 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 181 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.0170 chunk 186 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 ASN A 688 GLN B 462 ASN C 485 ASN D 96 GLN D 381 GLN E 27 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.117565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096216 restraints weight = 26813.251| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.89 r_work: 0.3264 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 16419 Z= 0.097 Angle : 0.479 7.120 22230 Z= 0.251 Chirality : 0.038 0.156 2538 Planarity : 0.003 0.039 2798 Dihedral : 8.242 87.414 2208 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.83 % Allowed : 10.65 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1928 helix: 1.29 (0.16), residues: 1128 sheet: 0.21 (0.37), residues: 188 loop : -1.26 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 255 TYR 0.017 0.001 TYR C 453 PHE 0.020 0.001 PHE E 328 TRP 0.049 0.002 TRP A 639 HIS 0.006 0.001 HIS C 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (16419) covalent geometry : angle 0.47864 / 0.25 (22230) hydrogen bonds : bond 0.03461 / 2.37 ( 809) hydrogen bonds : angle 3.65406 / 2.61 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.7994 (mp) cc_final: 0.7625 (mp) REVERT: A 571 MET cc_start: 0.8505 (tpp) cc_final: 0.8216 (mmt) REVERT: A 688 GLN cc_start: 0.7871 (tp40) cc_final: 0.6784 (tt0) REVERT: B 273 ARG cc_start: 0.7535 (mpt-90) cc_final: 0.7174 (mpt-90) REVERT: B 418 ILE cc_start: 0.7866 (tt) cc_final: 0.7377 (mt) REVERT: C 423 THR cc_start: 0.8483 (t) cc_final: 0.8268 (t) REVERT: C 605 ASN cc_start: 0.8038 (m-40) cc_final: 0.7795 (t0) REVERT: C 705 ARG cc_start: 0.6406 (mmp80) cc_final: 0.5612 (mmp-170) REVERT: D 113 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7043 (mm-30) REVERT: D 339 TYR cc_start: 0.6955 (m-10) cc_final: 0.6728 (m-10) REVERT: D 381 GLN cc_start: 0.8430 (tp40) cc_final: 0.8164 (tt0) outliers start: 15 outliers final: 9 residues processed: 199 average time/residue: 0.1250 time to fit residues: 37.2662 Evaluate side-chains 183 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 83 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 128 optimal weight: 0.3980 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN C 110 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093472 restraints weight = 26713.675| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.83 r_work: 0.3236 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16419 Z= 0.138 Angle : 0.522 13.011 22230 Z= 0.268 Chirality : 0.040 0.158 2538 Planarity : 0.004 0.037 2798 Dihedral : 8.212 87.022 2208 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 11.48 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1928 helix: 1.40 (0.16), residues: 1132 sheet: 0.16 (0.37), residues: 188 loop : -1.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.012 0.001 TYR B 454 PHE 0.020 0.001 PHE B 441 TRP 0.051 0.002 TRP A 639 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (16419) covalent geometry : angle 0.52166 / 0.27 (22230) hydrogen bonds : bond 0.04006 / 2.75 ( 809) hydrogen bonds : angle 3.66912 / 2.61 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8568 (tpp) cc_final: 0.8203 (mmt) REVERT: A 688 GLN cc_start: 0.7650 (tp40) cc_final: 0.6721 (tt0) REVERT: B 273 ARG cc_start: 0.7535 (mpt-90) cc_final: 0.7053 (mpt-90) REVERT: B 418 ILE cc_start: 0.8014 (tt) cc_final: 0.7531 (mt) REVERT: C 423 THR cc_start: 0.8465 (t) cc_final: 0.8245 (t) REVERT: C 462 MET cc_start: 0.7836 (mmm) cc_final: 0.7454 (mmt) REVERT: C 605 ASN cc_start: 0.8023 (m-40) cc_final: 0.7674 (t0) REVERT: C 705 ARG cc_start: 0.6405 (mmp80) cc_final: 0.5963 (mmp80) REVERT: D 113 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7119 (mm-30) REVERT: D 197 ASP cc_start: 0.8804 (p0) cc_final: 0.8428 (p0) REVERT: D 339 TYR cc_start: 0.7272 (m-10) cc_final: 0.6945 (m-10) outliers start: 23 outliers final: 15 residues processed: 201 average time/residue: 0.1406 time to fit residues: 41.6747 Evaluate side-chains 186 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 169 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 192 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095232 restraints weight = 26981.738| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.80 r_work: 0.3268 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16419 Z= 0.107 Angle : 0.476 6.329 22230 Z= 0.249 Chirality : 0.038 0.151 2538 Planarity : 0.003 0.035 2798 Dihedral : 7.850 87.041 2208 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.16 % Allowed : 12.42 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1928 helix: 1.52 (0.16), residues: 1133 sheet: 0.20 (0.38), residues: 188 loop : -1.17 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 564 TYR 0.010 0.001 TYR B 454 PHE 0.021 0.001 PHE E 328 TRP 0.056 0.002 TRP A 639 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16419) covalent geometry : angle 0.47620 / 0.25 (22230) hydrogen bonds : bond 0.03531 / 2.42 ( 809) hydrogen bonds : angle 3.54281 / 2.52 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 571 MET cc_start: 0.8587 (tpp) cc_final: 0.8277 (mmt) REVERT: A 688 GLN cc_start: 0.7658 (tp40) cc_final: 0.6781 (tt0) REVERT: A 752 MET cc_start: 0.8013 (tpp) cc_final: 0.7786 (tpp) REVERT: B 273 ARG cc_start: 0.7516 (mpt-90) cc_final: 0.7025 (mpt-90) REVERT: B 418 ILE cc_start: 0.7980 (tt) cc_final: 0.7494 (mt) REVERT: C 423 THR cc_start: 0.8392 (t) cc_final: 0.8167 (t) REVERT: C 449 ASP cc_start: 0.4860 (m-30) cc_final: 0.4647 (m-30) REVERT: C 462 MET cc_start: 0.8293 (mmm) cc_final: 0.8065 (mmt) REVERT: C 605 ASN cc_start: 0.8023 (m-40) cc_final: 0.7666 (t0) REVERT: C 705 ARG cc_start: 0.6457 (mmp80) cc_final: 0.5664 (mmp-170) REVERT: D 113 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7128 (mm-30) REVERT: D 197 ASP cc_start: 0.8768 (p0) cc_final: 0.8394 (p0) REVERT: D 339 TYR cc_start: 0.7155 (m-10) cc_final: 0.6903 (m-10) REVERT: D 381 GLN cc_start: 0.8389 (tp40) cc_final: 0.8158 (tp40) outliers start: 21 outliers final: 14 residues processed: 203 average time/residue: 0.1248 time to fit residues: 38.1501 Evaluate side-chains 184 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 185 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095116 restraints weight = 26947.510| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.78 r_work: 0.3269 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16419 Z= 0.106 Angle : 0.492 14.649 22230 Z= 0.254 Chirality : 0.038 0.150 2538 Planarity : 0.003 0.035 2798 Dihedral : 7.701 88.258 2208 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.44 % Allowed : 12.81 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1928 helix: 1.58 (0.16), residues: 1135 sheet: 0.22 (0.38), residues: 188 loop : -1.13 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 564 TYR 0.015 0.001 TYR A 565 PHE 0.023 0.001 PHE E 328 TRP 0.065 0.002 TRP A 639 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16419) covalent geometry : angle 0.49218 / 0.25 (22230) hydrogen bonds : bond 0.03454 / 2.36 ( 809) hydrogen bonds : angle 3.50680 / 2.49 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.636 Fit side-chains REVERT: A 571 MET cc_start: 0.8612 (tpp) cc_final: 0.8318 (mmt) REVERT: A 688 GLN cc_start: 0.7548 (tp40) cc_final: 0.6659 (tt0) REVERT: B 273 ARG cc_start: 0.7518 (mpt-90) cc_final: 0.7016 (mpt-90) REVERT: B 418 ILE cc_start: 0.7922 (tt) cc_final: 0.7436 (mt) REVERT: C 423 THR cc_start: 0.8341 (t) cc_final: 0.8112 (t) REVERT: C 462 MET cc_start: 0.8311 (mmm) cc_final: 0.7941 (mmt) REVERT: C 605 ASN cc_start: 0.8023 (m-40) cc_final: 0.7651 (t0) REVERT: C 705 ARG cc_start: 0.6440 (mmp80) cc_final: 0.5647 (mmp-170) REVERT: D 105 ILE cc_start: 0.8548 (pt) cc_final: 0.8324 (mt) REVERT: D 113 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7107 (mm-30) REVERT: D 197 ASP cc_start: 0.8757 (p0) cc_final: 0.8374 (p0) REVERT: D 339 TYR cc_start: 0.7184 (m-10) cc_final: 0.6906 (m-10) REVERT: D 381 GLN cc_start: 0.8281 (tp40) cc_final: 0.8069 (tt0) outliers start: 26 outliers final: 18 residues processed: 207 average time/residue: 0.1283 time to fit residues: 39.2115 Evaluate side-chains 192 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 75 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 ASN B 394 ASN ** C 636 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 = 0.3671 r_free = 0.3671 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094099 restraints weight = 27086.165| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.79 r_work: 0.3248 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16419 Z= 0.124 Angle : 0.507 10.083 22230 Z= 0.261 Chirality : 0.039 0.152 2538 Planarity : 0.003 0.036 2798 Dihedral : 7.800 89.992 2208 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.28 % Allowed : 13.20 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1928 helix: 1.59 (0.16), residues: 1132 sheet: 0.20 (0.38), residues: 188 loop : -1.18 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 564 TYR 0.014 0.001 TYR A 683 PHE 0.021 0.001 PHE E 328 TRP 0.056 0.002 TRP A 639 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (16419) covalent geometry : angle 0.50730 / 0.26 (22230) hydrogen bonds : bond 0.03722 / 2.55 ( 809) hydrogen bonds : angle 3.55653 / 2.52 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.596 Fit side-chains REVERT: A 571 MET cc_start: 0.8634 (tpp) cc_final: 0.8323 (mmt) REVERT: B 273 ARG cc_start: 0.7564 (mpt-90) cc_final: 0.7084 (mpt-90) REVERT: B 418 ILE cc_start: 0.8028 (tt) cc_final: 0.7508 (mt) REVERT: C 423 THR cc_start: 0.8379 (t) cc_final: 0.8142 (t) REVERT: C 605 ASN cc_start: 0.8017 (m-40) cc_final: 0.7623 (t0) REVERT: C 705 ARG cc_start: 0.6442 (mmp80) cc_final: 0.6050 (mmp80) REVERT: D 105 ILE cc_start: 0.8513 (pt) cc_final: 0.8277 (mt) REVERT: D 197 ASP cc_start: 0.8772 (p0) cc_final: 0.8390 (p0) REVERT: D 339 TYR cc_start: 0.7259 (m-10) cc_final: 0.6952 (m-10) outliers start: 23 outliers final: 18 residues processed: 193 average time/residue: 0.1331 time to fit residues: 38.0740 Evaluate side-chains 189 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.0030 chunk 2 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN C 66 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.116093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095554 restraints weight = 26910.959| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.76 r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16419 Z= 0.102 Angle : 0.507 16.042 22230 Z= 0.258 Chirality : 0.038 0.153 2538 Planarity : 0.003 0.033 2798 Dihedral : 7.568 89.584 2208 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.22 % Allowed : 13.64 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1928 helix: 1.70 (0.16), residues: 1127 sheet: 0.27 (0.38), residues: 188 loop : -1.14 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 564 TYR 0.016 0.001 TYR D 174 PHE 0.024 0.001 PHE E 328 TRP 0.052 0.002 TRP A 639 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (16419) covalent geometry : angle 0.50678 / 0.26 (22230) hydrogen bonds : bond 0.03323 / 2.27 ( 809) hydrogen bonds : angle 3.47025 / 2.46 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.392 Fit side-chains REVERT: A 571 MET cc_start: 0.8585 (tpp) cc_final: 0.8301 (mmt) REVERT: B 273 ARG cc_start: 0.7559 (mpt-90) cc_final: 0.7068 (mpt-90) REVERT: B 418 ILE cc_start: 0.7929 (tt) cc_final: 0.7423 (mt) REVERT: C 423 THR cc_start: 0.8327 (t) cc_final: 0.8093 (t) REVERT: C 605 ASN cc_start: 0.7979 (m-40) cc_final: 0.7608 (t0) REVERT: C 705 ARG cc_start: 0.6431 (mmp80) cc_final: 0.6058 (mmp80) REVERT: D 105 ILE cc_start: 0.8506 (pt) cc_final: 0.8279 (mt) REVERT: D 113 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7011 (mm-30) REVERT: D 197 ASP cc_start: 0.8760 (p0) cc_final: 0.8382 (p0) REVERT: D 339 TYR cc_start: 0.7116 (m-10) cc_final: 0.6817 (m-10) outliers start: 22 outliers final: 18 residues processed: 193 average time/residue: 0.1248 time to fit residues: 35.6511 Evaluate side-chains 186 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 173 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** C 636 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 = 0.3683 r_free = 0.3683 target = 0.115618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094897 restraints weight = 27154.086| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.80 r_work: 0.3249 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16419 Z= 0.112 Angle : 0.505 9.461 22230 Z= 0.260 Chirality : 0.039 0.164 2538 Planarity : 0.003 0.034 2798 Dihedral : 7.574 88.985 2208 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.16 % Allowed : 13.59 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1928 helix: 1.72 (0.16), residues: 1125 sheet: 0.27 (0.38), residues: 188 loop : -1.14 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 564 TYR 0.031 0.001 TYR C 453 PHE 0.025 0.001 PHE E 328 TRP 0.050 0.002 TRP A 639 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (16419) covalent geometry : angle 0.50515 / 0.26 (22230) hydrogen bonds : bond 0.03465 / 2.37 ( 809) hydrogen bonds : angle 3.48601 / 2.47 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.636 Fit side-chains REVERT: A 571 MET cc_start: 0.8597 (tpp) cc_final: 0.8315 (mmt) REVERT: B 418 ILE cc_start: 0.7977 (tt) cc_final: 0.7488 (mt) REVERT: C 423 THR cc_start: 0.8318 (t) cc_final: 0.8081 (t) REVERT: C 605 ASN cc_start: 0.8004 (m-40) cc_final: 0.7634 (t0) REVERT: C 705 ARG cc_start: 0.6435 (mmp80) cc_final: 0.6069 (mmp80) REVERT: D 105 ILE cc_start: 0.8502 (pt) cc_final: 0.8268 (mt) REVERT: D 113 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6984 (mm-30) REVERT: D 197 ASP cc_start: 0.8761 (p0) cc_final: 0.8363 (p0) REVERT: D 339 TYR cc_start: 0.7219 (m-10) cc_final: 0.6919 (m-10) REVERT: D 381 GLN cc_start: 0.8234 (tp40) cc_final: 0.7973 (tp40) outliers start: 21 outliers final: 19 residues processed: 188 average time/residue: 0.1289 time to fit residues: 36.2923 Evaluate side-chains 188 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 33 optimal weight: 0.0170 chunk 160 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** C 636 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 = 0.3689 r_free = 0.3689 target = 0.116052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095368 restraints weight = 27018.583| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.79 r_work: 0.3269 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16419 Z= 0.106 Angle : 0.510 12.439 22230 Z= 0.260 Chirality : 0.038 0.160 2538 Planarity : 0.003 0.034 2798 Dihedral : 7.479 88.548 2208 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.11 % Allowed : 13.92 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1928 helix: 1.74 (0.16), residues: 1127 sheet: 0.32 (0.38), residues: 188 loop : -1.10 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 564 TYR 0.016 0.001 TYR D 174 PHE 0.025 0.001 PHE E 328 TRP 0.048 0.002 TRP A 639 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16419) covalent geometry : angle 0.50953 / 0.26 (22230) hydrogen bonds : bond 0.03320 / 2.27 ( 809) hydrogen bonds : angle 3.44566 / 2.44 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.53 seconds wall clock time: 68 minutes 2.06 seconds (4082.06 seconds total)