Starting phenix.real_space_refine on Wed Mar 4 16:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpp_22418/03_2026/7jpp_22418.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9547 2.51 5 N 2516 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14872 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2515 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} Chain: "C" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4886 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} 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: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3312 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 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: 3.33, per 1000 atoms: 0.22 Number of scatterers: 14872 At special positions: 0 Unit cell: (93.09, 119.84, 154.08, 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 69 16.00 P 6 15.00 Mg 2 11.99 O 2732 8.00 N 2516 7.00 C 9547 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: 1.36 Conformation dependent library (CDL) restraints added in 459.5 milliseconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 7 sheets defined 64.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.602A pdb=" N THR A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 795 through 810 removed outlier: 3.664A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.602A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 829 " --> pdb=" O HIS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 860 removed outlier: 4.176A pdb=" N ASP A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.937A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 358 removed outlier: 4.120A pdb=" N GLU B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.186A pdb=" N SER B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 removed outlier: 3.713A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 removed outlier: 3.519A pdb=" N ALA B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.627A pdb=" N HIS B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 573 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.037A pdb=" N TYR C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 66 removed outlier: 4.034A pdb=" N PHE C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.575A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.861A pdb=" N GLY C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.563A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.126A pdb=" N HIS C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.521A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.563A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 339 removed outlier: 3.737A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 3.714A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.622A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.712A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.816A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.536A pdb=" N LEU C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.580A pdb=" N LEU C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 4.297A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.912A pdb=" N PHE C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 568 removed outlier: 3.633A pdb=" N LEU C 568 " --> pdb=" O VAL C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 584 through 593 removed outlier: 3.641A pdb=" N LEU C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.859A pdb=" N LEU C 600 " --> pdb=" O PRO C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 638 removed outlier: 3.812A pdb=" N LEU C 638 " --> pdb=" O TYR C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 Processing helix chain 'C' and resid 675 through 690 removed outlier: 3.689A pdb=" N LEU C 690 " --> pdb=" O SER C 686 " (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: 3.543A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.520A pdb=" N LEU D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.965A 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 160 through 166 Processing helix chain 'D' and resid 170 through 183 Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.856A pdb=" N LEU D 202 " --> 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 Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.842A pdb=" N LYS D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.813A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 290 removed outlier: 3.786A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.704A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.567A 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: 3.584A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.598A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.589A pdb=" N LYS D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 43 through 55 removed outlier: 3.607A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 98 through 111 removed outlier: 3.779A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.905A pdb=" N LYS E 116 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 131 removed outlier: 3.882A pdb=" N TYR E 129 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 131 " --> pdb=" O GLU E 128 " (cutoff:3.500A) 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 removed outlier: 3.651A pdb=" N LYS E 164 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 Processing helix chain 'E' and resid 221 through 232 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 249 through 267 Proline residue: E 259 - end of helix removed outlier: 4.010A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.811A pdb=" N LEU E 315 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.696A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.666A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 removed outlier: 3.956A pdb=" N TYR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 793 through 794 removed outlier: 3.928A pdb=" N ARG A 846 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 833 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.558A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 421 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 423 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.581A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.737A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.212A pdb=" N VAL E 59 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP E 125 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 61 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE E 33 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N SER E 158 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE E 35 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE E 179 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR E 36 " --> pdb=" O PHE E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 393 through 394 755 hydrogen bonds defined for protein. 2223 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: 2.38 Time building geometry restraints manager: 1.76 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: 4256 1.34 - 1.46: 2834 1.46 - 1.58: 7980 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 15184 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.42e+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 5.87e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP E 501 " pdb=" N7 ATP E 501 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 20312 4.38 - 8.75: 222 8.75 - 13.13: 15 13.13 - 17.51: 1 17.51 - 21.88: 2 Bond angle restraints: 20552 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 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.89 15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.79 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 118.19 8.61 1.00e+00 1.00e+00 7.41e+01 ... (remaining 20547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 8197 17.63 - 35.26: 814 35.26 - 52.88: 151 52.88 - 70.51: 45 70.51 - 88.14: 28 Dihedral angle restraints: 9235 sinusoidal: 3841 harmonic: 5394 Sorted by residual: dihedral pdb=" CA THR C 130 " pdb=" C THR C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLN D 358 " pdb=" C GLN D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2009 0.088 - 0.176: 303 0.176 - 0.264: 28 0.264 - 0.352: 2 0.352 - 0.441: 2 Chirality restraints: 2344 Sorted by residual: 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 2.20 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA LEU A 832 " pdb=" N LEU A 832 " pdb=" C LEU A 832 " pdb=" CB LEU A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 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 2.24 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2341 not shown) Planarity restraints: 2591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO E 239 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 44 " -0.007 2.00e-02 2.50e+03 2.23e-02 9.93e+00 pdb=" CG TYR D 44 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 44 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 44 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 44 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 44 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 44 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 44 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 122 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C THR C 122 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 122 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU C 123 " -0.018 2.00e-02 2.50e+03 ... (remaining 2588 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 84 2.63 - 3.20: 12602 3.20 - 3.76: 22691 3.76 - 4.33: 30253 4.33 - 4.90: 49568 Nonbonded interactions: 115198 Sorted by model distance: nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.061 2.170 nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR D 44 " pdb=" OE1 GLU D 83 " model vdw 2.235 3.040 nonbonded pdb=" O1A ATP E 501 " pdb="MG MG E 502 " model vdw 2.280 2.170 nonbonded pdb=" O LEU C 419 " pdb=" OG1 THR C 423 " model vdw 2.297 3.040 ... (remaining 115193 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 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: 2.360 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.080 15184 Z= 0.383 Angle : 1.181 21.883 20552 Z= 0.700 Chirality : 0.064 0.441 2344 Planarity : 0.007 0.094 2591 Dihedral : 15.662 88.139 5707 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -1.90 (0.17), residues: 1786 helix: -0.84 (0.14), residues: 1054 sheet: -0.61 (0.41), residues: 131 loop : -1.96 (0.22), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 533 TYR 0.050 0.003 TYR D 44 PHE 0.043 0.004 PHE B 539 TRP 0.046 0.003 TRP E 162 HIS 0.013 0.002 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00704 (15184) covalent geometry : angle 1.18068 (20552) hydrogen bonds : bond 0.17287 ( 755) hydrogen bonds : angle 6.44418 ( 2223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 815 THR cc_start: 0.7774 (p) cc_final: 0.7104 (p) REVERT: A 820 MET cc_start: 0.8113 (tpp) cc_final: 0.7854 (tpp) REVERT: B 288 LYS cc_start: 0.8007 (tppt) cc_final: 0.7687 (tptt) REVERT: B 557 LEU cc_start: 0.7192 (tp) cc_final: 0.6856 (tp) REVERT: C 29 TYR cc_start: 0.8132 (m-80) cc_final: 0.7926 (m-80) REVERT: C 148 LEU cc_start: 0.8794 (mp) cc_final: 0.8579 (mm) REVERT: C 369 LEU cc_start: 0.8533 (tp) cc_final: 0.8215 (mt) REVERT: C 372 PHE cc_start: 0.7773 (t80) cc_final: 0.7530 (t80) REVERT: C 467 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7923 (mp0) REVERT: C 673 MET cc_start: 0.4573 (tmm) cc_final: 0.4257 (tmm) REVERT: D 50 LEU cc_start: 0.8803 (tt) cc_final: 0.8170 (mp) REVERT: D 138 PHE cc_start: 0.6761 (t80) cc_final: 0.6542 (t80) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1375 time to fit residues: 60.7424 Evaluate side-chains 176 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 411 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN C 87 ASN C 128 ASN C 149 GLN E 48 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107104 restraints weight = 24788.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108443 restraints weight = 15327.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109717 restraints weight = 12150.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110026 restraints weight = 10072.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110340 restraints weight = 9585.158| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15184 Z= 0.142 Angle : 0.597 10.338 20552 Z= 0.314 Chirality : 0.041 0.140 2344 Planarity : 0.004 0.064 2591 Dihedral : 8.084 83.546 2017 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.73 % Allowed : 7.27 % Favored : 91.00 % 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: -0.56 (0.19), residues: 1786 helix: 0.43 (0.15), residues: 1086 sheet: -0.24 (0.43), residues: 124 loop : -1.87 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 273 TYR 0.015 0.002 TYR E 204 PHE 0.036 0.002 PHE C 497 TRP 0.011 0.001 TRP E 162 HIS 0.008 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00322 (15184) covalent geometry : angle 0.59662 (20552) hydrogen bonds : bond 0.04899 ( 755) hydrogen bonds : angle 4.28677 ( 2223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ARG cc_start: 0.7019 (tpm170) cc_final: 0.5924 (tpm170) REVERT: B 288 LYS cc_start: 0.8104 (tppt) cc_final: 0.7677 (tptt) REVERT: B 557 LEU cc_start: 0.7030 (tp) cc_final: 0.6788 (tp) REVERT: C 369 LEU cc_start: 0.8417 (tp) cc_final: 0.8164 (mt) REVERT: D 50 LEU cc_start: 0.8991 (tt) cc_final: 0.8342 (mp) outliers start: 29 outliers final: 13 residues processed: 231 average time/residue: 0.1279 time to fit residues: 43.3612 Evaluate side-chains 173 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 172 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.129360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105523 restraints weight = 24964.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108249 restraints weight = 15460.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108969 restraints weight = 10895.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109239 restraints weight = 9879.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109496 restraints weight = 9465.357| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15184 Z= 0.133 Angle : 0.547 9.292 20552 Z= 0.289 Chirality : 0.040 0.168 2344 Planarity : 0.004 0.050 2591 Dihedral : 7.362 86.903 2017 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 10.14 % Favored : 87.90 % 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: 0.07 (0.19), residues: 1786 helix: 0.99 (0.16), residues: 1091 sheet: 0.18 (0.45), residues: 114 loop : -1.78 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 786 TYR 0.020 0.001 TYR B 508 PHE 0.021 0.002 PHE E 203 TRP 0.008 0.001 TRP E 162 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00304 (15184) covalent geometry : angle 0.54717 (20552) hydrogen bonds : bond 0.04332 ( 755) hydrogen bonds : angle 4.02804 ( 2223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8364 (tpp) cc_final: 0.7982 (tpp) REVERT: B 273 ARG cc_start: 0.7067 (tpm170) cc_final: 0.5994 (tpm170) REVERT: B 288 LYS cc_start: 0.8109 (tppt) cc_final: 0.7706 (tptt) REVERT: B 498 TYR cc_start: 0.8243 (t80) cc_final: 0.7970 (t80) REVERT: B 557 LEU cc_start: 0.7045 (tp) cc_final: 0.6781 (tp) REVERT: C 29 TYR cc_start: 0.8333 (m-80) cc_final: 0.7936 (m-10) REVERT: C 369 LEU cc_start: 0.8471 (tp) cc_final: 0.8230 (mp) REVERT: C 673 MET cc_start: 0.4516 (ppp) cc_final: 0.4221 (ppp) REVERT: D 50 LEU cc_start: 0.9001 (tt) cc_final: 0.8342 (mp) REVERT: E 94 ILE cc_start: 0.7723 (mm) cc_final: 0.7438 (pt) outliers start: 33 outliers final: 18 residues processed: 198 average time/residue: 0.1189 time to fit residues: 35.4245 Evaluate side-chains 172 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 139 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.130113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105776 restraints weight = 24905.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108576 restraints weight = 15390.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110500 restraints weight = 11114.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111773 restraints weight = 8939.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112637 restraints weight = 7706.770| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15184 Z= 0.111 Angle : 0.503 8.803 20552 Z= 0.265 Chirality : 0.038 0.155 2344 Planarity : 0.004 0.046 2591 Dihedral : 6.995 89.180 2017 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.79 % Allowed : 11.51 % Favored : 86.70 % 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: 0.49 (0.20), residues: 1786 helix: 1.35 (0.16), residues: 1096 sheet: 0.33 (0.45), residues: 114 loop : -1.73 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 786 TYR 0.017 0.001 TYR C 179 PHE 0.021 0.001 PHE E 328 TRP 0.008 0.001 TRP C 448 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00242 (15184) covalent geometry : angle 0.50333 (20552) hydrogen bonds : bond 0.03754 ( 755) hydrogen bonds : angle 3.80322 ( 2223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 820 MET cc_start: 0.8317 (tpp) cc_final: 0.7888 (tpp) REVERT: B 273 ARG cc_start: 0.7018 (tpm170) cc_final: 0.5994 (tpm170) REVERT: B 288 LYS cc_start: 0.8138 (tppt) cc_final: 0.7765 (tptt) REVERT: B 557 LEU cc_start: 0.7030 (tp) cc_final: 0.6802 (tp) REVERT: C 262 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 369 LEU cc_start: 0.8404 (tp) cc_final: 0.8194 (mp) REVERT: D 50 LEU cc_start: 0.8969 (tt) cc_final: 0.8321 (mp) outliers start: 30 outliers final: 16 residues processed: 206 average time/residue: 0.1185 time to fit residues: 36.8240 Evaluate side-chains 177 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 94 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 339 GLN D 104 GLN D 381 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104950 restraints weight = 24528.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107806 restraints weight = 14926.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109818 restraints weight = 10791.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111112 restraints weight = 8634.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111887 restraints weight = 7460.548| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15184 Z= 0.131 Angle : 0.526 9.453 20552 Z= 0.276 Chirality : 0.039 0.140 2344 Planarity : 0.004 0.048 2591 Dihedral : 6.939 83.868 2017 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 12.64 % Favored : 85.51 % 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 (0.20), residues: 1786 helix: 1.44 (0.16), residues: 1096 sheet: 0.42 (0.45), residues: 114 loop : -1.75 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.020 0.001 TYR B 508 PHE 0.020 0.001 PHE E 203 TRP 0.008 0.001 TRP D 428 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00305 (15184) covalent geometry : angle 0.52551 (20552) hydrogen bonds : bond 0.03978 ( 755) hydrogen bonds : angle 3.81591 ( 2223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.599 Fit side-chains REVERT: A 815 THR cc_start: 0.7856 (p) cc_final: 0.7650 (p) REVERT: A 820 MET cc_start: 0.8322 (tpp) cc_final: 0.7862 (tpp) REVERT: B 273 ARG cc_start: 0.6895 (tpm170) cc_final: 0.5883 (tpm170) REVERT: B 288 LYS cc_start: 0.8108 (tppt) cc_final: 0.7755 (tptt) REVERT: B 557 LEU cc_start: 0.6985 (tp) cc_final: 0.6761 (tp) REVERT: B 562 ASP cc_start: 0.7273 (t0) cc_final: 0.6949 (t0) REVERT: C 262 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 50 LEU cc_start: 0.8953 (tt) cc_final: 0.8320 (mp) outliers start: 31 outliers final: 21 residues processed: 188 average time/residue: 0.1050 time to fit residues: 30.8932 Evaluate side-chains 171 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 133 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN ** E 75 GLN ** 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 = 0.3690 r_free = 0.3690 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105556 restraints weight = 24798.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108267 restraints weight = 15417.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110132 restraints weight = 11227.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111319 restraints weight = 9060.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112246 restraints weight = 7879.709| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15184 Z= 0.107 Angle : 0.501 12.337 20552 Z= 0.260 Chirality : 0.038 0.140 2344 Planarity : 0.003 0.049 2591 Dihedral : 6.684 81.633 2017 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 13.24 % Favored : 85.15 % 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: 0.71 (0.20), residues: 1786 helix: 1.57 (0.16), residues: 1099 sheet: 0.50 (0.46), residues: 114 loop : -1.77 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.011 0.001 TYR B 508 PHE 0.023 0.001 PHE E 328 TRP 0.006 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00239 (15184) covalent geometry : angle 0.50109 (20552) hydrogen bonds : bond 0.03550 ( 755) hydrogen bonds : angle 3.65540 ( 2223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.569 Fit side-chains REVERT: A 815 THR cc_start: 0.7871 (p) cc_final: 0.7658 (p) REVERT: A 820 MET cc_start: 0.8346 (tpp) cc_final: 0.7889 (tpp) REVERT: B 273 ARG cc_start: 0.6955 (tpm170) cc_final: 0.5970 (tpm170) REVERT: B 288 LYS cc_start: 0.8076 (tppt) cc_final: 0.7751 (tptt) REVERT: C 262 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8304 (mp) REVERT: D 50 LEU cc_start: 0.8974 (tt) cc_final: 0.8337 (mp) outliers start: 27 outliers final: 18 residues processed: 184 average time/residue: 0.1198 time to fit residues: 33.3873 Evaluate side-chains 168 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 176 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 GLN D 216 HIS D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103073 restraints weight = 24467.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105839 restraints weight = 15088.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107716 restraints weight = 10913.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108917 restraints weight = 8832.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109623 restraints weight = 7687.636| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15184 Z= 0.156 Angle : 0.564 11.247 20552 Z= 0.294 Chirality : 0.040 0.139 2344 Planarity : 0.004 0.042 2591 Dihedral : 6.931 80.972 2017 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.97 % Allowed : 13.54 % Favored : 84.50 % 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: 0.53 (0.20), residues: 1786 helix: 1.43 (0.16), residues: 1097 sheet: 0.38 (0.45), residues: 114 loop : -1.82 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 786 TYR 0.019 0.002 TYR B 508 PHE 0.024 0.002 PHE E 203 TRP 0.008 0.001 TRP C 51 HIS 0.006 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00370 (15184) covalent geometry : angle 0.56443 (20552) hydrogen bonds : bond 0.04345 ( 755) hydrogen bonds : angle 3.89700 ( 2223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 815 THR cc_start: 0.7877 (p) cc_final: 0.7675 (p) REVERT: A 820 MET cc_start: 0.8333 (tpp) cc_final: 0.7890 (tpp) REVERT: B 288 LYS cc_start: 0.8136 (tppt) cc_final: 0.7761 (tptt) REVERT: B 562 ASP cc_start: 0.7283 (t0) cc_final: 0.6967 (t0) REVERT: C 32 LYS cc_start: 0.5736 (ptmt) cc_final: 0.5439 (tptt) REVERT: C 262 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8251 (mp) REVERT: D 50 LEU cc_start: 0.9015 (tt) cc_final: 0.8380 (mp) outliers start: 33 outliers final: 24 residues processed: 184 average time/residue: 0.1124 time to fit residues: 31.7910 Evaluate side-chains 168 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 78 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.128214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103759 restraints weight = 24488.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106554 restraints weight = 15035.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108462 restraints weight = 10848.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109665 restraints weight = 8744.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110579 restraints weight = 7602.087| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15184 Z= 0.132 Angle : 0.543 11.567 20552 Z= 0.278 Chirality : 0.039 0.179 2344 Planarity : 0.004 0.041 2591 Dihedral : 6.834 82.995 2017 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.85 % Allowed : 13.77 % Favored : 84.38 % 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: 0.59 (0.20), residues: 1786 helix: 1.48 (0.16), residues: 1099 sheet: 0.36 (0.45), residues: 114 loop : -1.80 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 786 TYR 0.015 0.001 TYR C 29 PHE 0.021 0.001 PHE C 372 TRP 0.007 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00311 (15184) covalent geometry : angle 0.54264 (20552) hydrogen bonds : bond 0.03944 ( 755) hydrogen bonds : angle 3.80370 ( 2223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8307 (tpp) cc_final: 0.7849 (tpp) REVERT: B 288 LYS cc_start: 0.8133 (tppt) cc_final: 0.7781 (tptt) REVERT: B 562 ASP cc_start: 0.7436 (t0) cc_final: 0.7146 (t0) REVERT: C 32 LYS cc_start: 0.5666 (ptmt) cc_final: 0.5406 (tptt) REVERT: D 50 LEU cc_start: 0.8999 (tt) cc_final: 0.8362 (mp) outliers start: 31 outliers final: 23 residues processed: 182 average time/residue: 0.1119 time to fit residues: 31.6975 Evaluate side-chains 166 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 0.0070 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 GLN E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105043 restraints weight = 24984.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107729 restraints weight = 15566.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109593 restraints weight = 11288.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110712 restraints weight = 9091.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111468 restraints weight = 7915.244| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15184 Z= 0.104 Angle : 0.510 10.965 20552 Z= 0.263 Chirality : 0.038 0.137 2344 Planarity : 0.003 0.040 2591 Dihedral : 6.558 82.489 2017 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.31 % Allowed : 14.91 % Favored : 83.78 % 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: 0.82 (0.20), residues: 1786 helix: 1.67 (0.16), residues: 1096 sheet: 0.34 (0.46), residues: 109 loop : -1.68 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 786 TYR 0.018 0.001 TYR B 508 PHE 0.025 0.001 PHE B 492 TRP 0.007 0.001 TRP B 443 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00230 (15184) covalent geometry : angle 0.50963 (20552) hydrogen bonds : bond 0.03429 ( 755) hydrogen bonds : angle 3.66541 ( 2223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8324 (tpp) cc_final: 0.7872 (tpp) REVERT: B 288 LYS cc_start: 0.8215 (tppt) cc_final: 0.7840 (tptt) REVERT: B 562 ASP cc_start: 0.7428 (t70) cc_final: 0.7133 (t0) outliers start: 22 outliers final: 19 residues processed: 181 average time/residue: 0.1184 time to fit residues: 32.5957 Evaluate side-chains 165 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 172 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 156 optimal weight: 0.0870 chunk 74 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105707 restraints weight = 24830.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108434 restraints weight = 15345.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110321 restraints weight = 11103.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111601 restraints weight = 8914.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112308 restraints weight = 7676.882| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15184 Z= 0.105 Angle : 0.550 14.954 20552 Z= 0.277 Chirality : 0.038 0.160 2344 Planarity : 0.003 0.040 2591 Dihedral : 6.433 82.399 2017 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.19 % Allowed : 15.50 % Favored : 83.30 % 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: 0.85 (0.20), residues: 1786 helix: 1.67 (0.16), residues: 1097 sheet: 0.44 (0.48), residues: 109 loop : -1.63 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 786 TYR 0.014 0.001 TYR C 29 PHE 0.020 0.001 PHE E 328 TRP 0.006 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00233 (15184) covalent geometry : angle 0.55036 (20552) hydrogen bonds : bond 0.03400 ( 755) hydrogen bonds : angle 3.65819 ( 2223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8315 (tpp) cc_final: 0.7884 (tpp) REVERT: B 288 LYS cc_start: 0.8200 (tppt) cc_final: 0.7837 (tptt) REVERT: B 363 MET cc_start: 0.5947 (ppp) cc_final: 0.5364 (mtm) REVERT: B 562 ASP cc_start: 0.7437 (t70) cc_final: 0.7146 (t0) REVERT: C 126 GLN cc_start: 0.7746 (mp10) cc_final: 0.7546 (mp10) REVERT: D 75 MET cc_start: 0.7941 (ppp) cc_final: 0.7719 (ppp) REVERT: D 390 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7344 (mtt90) outliers start: 20 outliers final: 19 residues processed: 179 average time/residue: 0.1169 time to fit residues: 31.9206 Evaluate side-chains 170 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 100 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 147 optimal weight: 0.1980 chunk 172 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107165 restraints weight = 24179.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110075 restraints weight = 14762.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112046 restraints weight = 10542.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113378 restraints weight = 8469.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114298 restraints weight = 7279.963| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15184 Z= 0.102 Angle : 0.554 13.424 20552 Z= 0.275 Chirality : 0.038 0.146 2344 Planarity : 0.003 0.040 2591 Dihedral : 6.325 82.557 2017 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.19 % Allowed : 15.74 % Favored : 83.06 % 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: 0.92 (0.20), residues: 1786 helix: 1.71 (0.16), residues: 1097 sheet: 0.48 (0.48), residues: 111 loop : -1.57 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 786 TYR 0.024 0.001 TYR B 508 PHE 0.025 0.001 PHE E 328 TRP 0.006 0.001 TRP B 443 HIS 0.006 0.000 HIS C 637 Details of bonding type rmsd covalent geometry : bond 0.00225 (15184) covalent geometry : angle 0.55414 (20552) hydrogen bonds : bond 0.03271 ( 755) hydrogen bonds : angle 3.61435 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2124.50 seconds wall clock time: 37 minutes 46.06 seconds (2266.06 seconds total)