Starting phenix.real_space_refine on Fri Jul 3 16:02:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpp_22418/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpp_22418/07_2026/7jpp_22418.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.97, per 1000 atoms: 0.20 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: 1.01 Conformation dependent library (CDL) restraints added in 507.0 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: 0.31 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: 1.97 Time building geometry restraints manager: 1.39 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: 8177 17.63 - 35.26: 791 35.26 - 52.88: 144 52.88 - 70.51: 37 70.51 - 88.14: 24 Dihedral angle restraints: 9173 sinusoidal: 3779 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 9170 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: 2.210 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 12.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 15.252 88.139 5645 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/Z covalent geometry : bond 0.00704 / 0.38 (15184) covalent geometry : angle 1.18068 / 0.70 (20552) hydrogen bonds : bond 0.17287 / 11.67 ( 755) hydrogen bonds : angle 6.44418 / 4.45 ( 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 : 0.607 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: 0.1210 time to fit residues: 54.1387 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 : 0.564 ------------------------------------------------------------------------------- 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... 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 = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106486 restraints weight = 24609.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109127 restraints weight = 15675.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110529 restraints weight = 10828.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111136 restraints weight = 9173.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111338 restraints weight = 8637.541| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1890 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 : 0.600 10.188 20552 Z= 0.315 Chirality : 0.041 0.144 2344 Planarity : 0.004 0.066 2591 Dihedral : 5.234 83.586 1955 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.67 % Allowed : 7.33 % 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: -0.57 (0.19), residues: 1786 helix: 0.42 (0.15), residues: 1086 sheet: -0.25 (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 0.037 0.002 PHE C 497 TRP 0.012 0.001 TRP C 448 HIS 0.007 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15184) covalent geometry : angle 0.59955 / 0.32 (20552) hydrogen bonds : bond 0.05016 / 3.36 ( 755) hydrogen bonds : angle 4.33873 / 3.01 ( 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 231 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ARG cc_start: 0.7025 (tpm170) cc_final: 0.5915 (tpm170) REVERT: B 288 LYS cc_start: 0.8094 (tppt) cc_final: 0.7665 (tptt) REVERT: B 557 LEU cc_start: 0.7010 (tp) cc_final: 0.6747 (tp) REVERT: C 369 LEU cc_start: 0.8425 (tp) cc_final: 0.8183 (mt) REVERT: D 50 LEU cc_start: 0.8973 (tt) cc_final: 0.8322 (mp) outliers start: 28 outliers final: 12 residues processed: 224 average time/residue: 0.1139 time to fit residues: 38.1133 Evaluate side-chains 171 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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: 0.0980 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104686 restraints weight = 24866.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107567 restraints weight = 15434.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109530 restraints weight = 11183.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110870 restraints weight = 9026.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111768 restraints weight = 7792.836| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15184 Z= 0.149 Angle : 0.563 9.392 20552 Z= 0.299 Chirality : 0.040 0.145 2344 Planarity : 0.004 0.049 2591 Dihedral : 4.945 79.655 1955 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.03 % Allowed : 9.90 % Favored : 88.07 % 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: 0.00 (0.19), residues: 1786 helix: 0.93 (0.16), residues: 1091 sheet: 0.13 (0.44), residues: 114 loop : -1.81 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 30 TYR 0.020 0.002 TYR B 508 PHE 0.023 0.002 PHE E 203 TRP 0.009 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15184) covalent geometry : angle 0.56315 / 0.30 (20552) hydrogen bonds : bond 0.04544 / 3.08 ( 755) hydrogen bonds : angle 4.08479 / 2.86 ( 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 210 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 820 MET cc_start: 0.8342 (tpp) cc_final: 0.7989 (tpp) REVERT: B 273 ARG cc_start: 0.6998 (tpm170) cc_final: 0.6020 (tpm170) REVERT: B 288 LYS cc_start: 0.8116 (tppt) cc_final: 0.7746 (tptt) REVERT: B 498 TYR cc_start: 0.8293 (t80) cc_final: 0.8047 (t80) REVERT: B 557 LEU cc_start: 0.7016 (tp) cc_final: 0.6757 (tp) REVERT: C 29 TYR cc_start: 0.8262 (m-80) cc_final: 0.7852 (m-10) REVERT: C 262 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (mp) REVERT: C 369 LEU cc_start: 0.8445 (tp) cc_final: 0.8233 (mp) REVERT: C 673 MET cc_start: 0.4594 (ppp) cc_final: 0.4282 (ppp) REVERT: D 50 LEU cc_start: 0.8970 (tt) cc_final: 0.8318 (mp) REVERT: E 94 ILE cc_start: 0.7774 (mm) cc_final: 0.7483 (pt) outliers start: 34 outliers final: 18 residues processed: 199 average time/residue: 0.1145 time to fit residues: 34.6121 Evaluate side-chains 172 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 359 VAL 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 262 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 201 LEU 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: 0.7980 chunk 174 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3679 r_free = 0.3679 target = 0.128830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105283 restraints weight = 25053.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107996 restraints weight = 15385.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108855 restraints weight = 10610.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109028 restraints weight = 9775.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109314 restraints weight = 9278.905| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15184 Z= 0.120 Angle : 0.518 8.890 20552 Z= 0.272 Chirality : 0.039 0.151 2344 Planarity : 0.004 0.047 2591 Dihedral : 4.684 70.927 1955 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 11.81 % Favored : 86.34 % 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: 0.37 (0.20), residues: 1786 helix: 1.25 (0.16), residues: 1098 sheet: 0.33 (0.45), residues: 114 loop : -1.77 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.021 0.001 TYR C 179 PHE 0.022 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/Z covalent geometry : bond 0.00270 / 0.12 (15184) covalent geometry : angle 0.51846 / 0.27 (20552) hydrogen bonds : bond 0.03959 / 2.67 ( 755) hydrogen bonds : angle 3.83639 / 2.68 ( 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 211 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.695 Fit side-chains REVERT: A 820 MET cc_start: 0.8317 (tpp) cc_final: 0.7898 (tpp) REVERT: B 273 ARG cc_start: 0.7100 (tpm170) cc_final: 0.6015 (tpm170) REVERT: B 288 LYS cc_start: 0.8151 (tppt) cc_final: 0.7730 (tptt) REVERT: B 557 LEU cc_start: 0.7088 (tp) cc_final: 0.6850 (tp) REVERT: B 562 ASP cc_start: 0.7351 (t0) cc_final: 0.7035 (t0) REVERT: C 262 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 612 LYS cc_start: 0.5803 (mmtp) cc_final: 0.5462 (ptpp) REVERT: D 50 LEU cc_start: 0.8975 (tt) cc_final: 0.8312 (mp) REVERT: D 401 LEU cc_start: 0.8744 (mt) cc_final: 0.8540 (mt) REVERT: E 149 ASP cc_start: 0.6041 (t70) cc_final: 0.5738 (t70) outliers start: 31 outliers final: 17 residues processed: 204 average time/residue: 0.1140 time to fit residues: 35.3418 Evaluate side-chains 175 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 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 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: 0.0570 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 170 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 339 GLN C 379 GLN D 104 GLN D 216 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104174 restraints weight = 24539.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107026 restraints weight = 14981.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109032 restraints weight = 10775.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110304 restraints weight = 8621.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111190 restraints weight = 7457.625| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15184 Z= 0.134 Angle : 0.534 9.457 20552 Z= 0.279 Chirality : 0.039 0.186 2344 Planarity : 0.004 0.049 2591 Dihedral : 4.575 64.107 1955 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.91 % Allowed : 12.58 % 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: 0.49 (0.20), residues: 1786 helix: 1.36 (0.16), residues: 1097 sheet: 0.44 (0.45), residues: 114 loop : -1.76 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.025 0.001 TYR C 179 PHE 0.021 0.002 PHE E 203 TRP 0.008 0.001 TRP D 428 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15184) covalent geometry : angle 0.53373 / 0.28 (20552) hydrogen bonds : bond 0.04070 / 2.75 ( 755) hydrogen bonds : angle 3.84600 / 2.68 ( 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 200 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8234 (tp30) cc_final: 0.7938 (tp30) REVERT: A 815 THR cc_start: 0.7835 (p) cc_final: 0.7625 (p) REVERT: A 820 MET cc_start: 0.8327 (tpp) cc_final: 0.7869 (tpp) REVERT: B 288 LYS cc_start: 0.8108 (tppt) cc_final: 0.7761 (tptt) REVERT: B 557 LEU cc_start: 0.7001 (tp) cc_final: 0.6776 (tp) REVERT: B 562 ASP cc_start: 0.7297 (t0) cc_final: 0.6975 (t0) REVERT: C 32 LYS cc_start: 0.5483 (ptmt) cc_final: 0.5134 (tptt) REVERT: C 262 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 612 LYS cc_start: 0.5987 (mmtp) cc_final: 0.5675 (ptpp) REVERT: D 50 LEU cc_start: 0.8992 (tt) cc_final: 0.8377 (mp) outliers start: 32 outliers final: 22 residues processed: 193 average time/residue: 0.0989 time to fit residues: 29.5828 Evaluate side-chains 170 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 B residue 336 HIS Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 439 SER 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 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 201 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 329 ILE 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: 1.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 69 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3721 r_free = 0.3721 target = 0.132354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107894 restraints weight = 24133.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110834 restraints weight = 14629.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112880 restraints weight = 10486.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114026 restraints weight = 8353.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115048 restraints weight = 7244.845| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3348 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= 0.096 Angle : 0.488 9.258 20552 Z= 0.253 Chirality : 0.038 0.142 2344 Planarity : 0.003 0.043 2591 Dihedral : 4.271 50.149 1955 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.37 % Allowed : 13.54 % Favored : 85.09 % 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: 0.77 (0.20), residues: 1786 helix: 1.59 (0.16), residues: 1102 sheet: 0.62 (0.46), residues: 114 loop : -1.72 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 786 TYR 0.013 0.001 TYR B 508 PHE 0.014 0.001 PHE E 203 TRP 0.008 0.001 TRP B 443 HIS 0.006 0.000 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (15184) covalent geometry : angle 0.48752 / 0.25 (20552) hydrogen bonds : bond 0.03267 / 2.19 ( 755) hydrogen bonds : angle 3.62516 / 2.52 ( 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 195 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.471 Fit side-chains REVERT: A 784 GLU cc_start: 0.8256 (tp30) cc_final: 0.8006 (tp30) REVERT: A 815 THR cc_start: 0.7808 (p) cc_final: 0.7600 (p) REVERT: A 820 MET cc_start: 0.8334 (tpp) cc_final: 0.7887 (tpp) REVERT: B 273 ARG cc_start: 0.6940 (tpm170) cc_final: 0.6096 (tpm170) REVERT: B 288 LYS cc_start: 0.8066 (tppt) cc_final: 0.7776 (mtmm) REVERT: B 562 ASP cc_start: 0.7329 (t0) cc_final: 0.7033 (t0) REVERT: C 144 MET cc_start: 0.7981 (tpt) cc_final: 0.7609 (tpt) REVERT: D 50 LEU cc_start: 0.8990 (tt) cc_final: 0.8353 (mp) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.1108 time to fit residues: 32.0100 Evaluate side-chains 164 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 455 THR Chi-restraints excluded: chain C residue 429 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 176 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 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 = 0.3699 r_free = 0.3699 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106438 restraints weight = 24241.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109310 restraints weight = 14864.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111228 restraints weight = 10680.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112363 restraints weight = 8615.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113352 restraints weight = 7496.838| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3470 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 : 0.498 10.568 20552 Z= 0.258 Chirality : 0.038 0.143 2344 Planarity : 0.003 0.042 2591 Dihedral : 4.173 48.039 1955 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.49 % Allowed : 14.25 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1786 helix: 1.66 (0.16), residues: 1099 sheet: 0.52 (0.48), residues: 109 loop : -1.68 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 786 TYR 0.021 0.001 TYR B 508 PHE 0.020 0.001 PHE C 372 TRP 0.006 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15184) covalent geometry : angle 0.49754 / 0.26 (20552) hydrogen bonds : bond 0.03487 / 2.35 ( 755) hydrogen bonds : angle 3.65969 / 2.55 ( 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 182 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8344 (tpp) cc_final: 0.7890 (tpp) REVERT: B 288 LYS cc_start: 0.8072 (tppt) cc_final: 0.7785 (mtmm) REVERT: B 562 ASP cc_start: 0.7313 (t0) cc_final: 0.7021 (t0) REVERT: C 262 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8275 (mp) REVERT: D 50 LEU cc_start: 0.8987 (tt) cc_final: 0.8358 (mp) REVERT: E 203 PHE cc_start: 0.7565 (t80) cc_final: 0.7362 (t80) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.1167 time to fit residues: 31.5036 Evaluate side-chains 164 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 429 TYR 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 247 GLU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 75 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 78 optimal weight: 0.0070 chunk 103 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3703 r_free = 0.3703 target = 0.131060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106408 restraints weight = 24390.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109303 restraints weight = 14936.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111046 restraints weight = 10742.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112476 restraints weight = 8712.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113322 restraints weight = 7511.190| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3572 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= 0.105 Angle : 0.510 12.274 20552 Z= 0.260 Chirality : 0.038 0.142 2344 Planarity : 0.003 0.041 2591 Dihedral : 4.122 47.661 1955 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.43 % Allowed : 14.73 % Favored : 83.84 % 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: 0.90 (0.20), residues: 1786 helix: 1.71 (0.16), residues: 1099 sheet: 0.56 (0.48), residues: 109 loop : -1.65 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 786 TYR 0.010 0.001 TYR C 29 PHE 0.026 0.001 PHE B 492 TRP 0.005 0.001 TRP C 51 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15184) covalent geometry : angle 0.51023 / 0.26 (20552) hydrogen bonds : bond 0.03394 / 2.29 ( 755) hydrogen bonds : angle 3.62538 / 2.52 ( 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 184 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 784 GLU cc_start: 0.8161 (tp30) cc_final: 0.7947 (tp30) REVERT: A 820 MET cc_start: 0.8363 (tpp) cc_final: 0.7884 (tpp) REVERT: B 288 LYS cc_start: 0.8094 (tppt) cc_final: 0.7785 (mtmm) REVERT: B 562 ASP cc_start: 0.7313 (t0) cc_final: 0.7016 (t0) REVERT: C 262 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 50 LEU cc_start: 0.8972 (tt) cc_final: 0.8353 (mp) REVERT: E 203 PHE cc_start: 0.7439 (t80) cc_final: 0.7207 (t80) outliers start: 24 outliers final: 16 residues processed: 182 average time/residue: 0.1192 time to fit residues: 33.0062 Evaluate side-chains 166 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 262 LEU Chi-restraints excluded: chain C residue 429 TYR 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 247 GLU 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 396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 0.0060 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107187 restraints weight = 24303.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110120 restraints weight = 14755.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112060 restraints weight = 10539.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113380 restraints weight = 8494.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114233 restraints weight = 7309.758| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15184 Z= 0.102 Angle : 0.535 13.580 20552 Z= 0.266 Chirality : 0.038 0.178 2344 Planarity : 0.003 0.041 2591 Dihedral : 4.059 47.426 1955 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.43 % Allowed : 15.15 % Favored : 83.42 % 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: 0.94 (0.20), residues: 1786 helix: 1.73 (0.16), residues: 1100 sheet: 0.58 (0.48), residues: 111 loop : -1.61 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 786 TYR 0.021 0.001 TYR B 508 PHE 0.022 0.001 PHE C 372 TRP 0.005 0.001 TRP E 162 HIS 0.006 0.001 HIS C 637 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15184) covalent geometry : angle 0.53489 / 0.27 (20552) hydrogen bonds : bond 0.03301 / 2.23 ( 755) hydrogen bonds : angle 3.61991 / 2.51 ( 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 186 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8371 (tpp) cc_final: 0.7882 (tpp) REVERT: B 288 LYS cc_start: 0.8089 (tppt) cc_final: 0.7772 (mtmm) REVERT: B 363 MET cc_start: 0.5919 (ppp) cc_final: 0.5706 (mtm) REVERT: B 562 ASP cc_start: 0.7347 (t0) cc_final: 0.7039 (t0) REVERT: C 32 LYS cc_start: 0.5569 (ptmt) cc_final: 0.5293 (tptt) REVERT: C 372 PHE cc_start: 0.7066 (t80) cc_final: 0.6824 (t80) REVERT: E 203 PHE cc_start: 0.7226 (t80) cc_final: 0.6979 (t80) outliers start: 24 outliers final: 17 residues processed: 183 average time/residue: 0.1163 time to fit residues: 32.4535 Evaluate side-chains 165 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain C residue 429 TYR 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 247 GLU Chi-restraints excluded: chain D residue 329 ILE 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 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 172 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 156 optimal weight: 0.0030 chunk 74 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 175 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3712 r_free = 0.3712 target = 0.131691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107098 restraints weight = 24269.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109993 restraints weight = 14703.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111947 restraints weight = 10550.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112893 restraints weight = 8477.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114003 restraints weight = 7461.922| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15184 Z= 0.107 Angle : 0.552 15.611 20552 Z= 0.274 Chirality : 0.038 0.166 2344 Planarity : 0.003 0.041 2591 Dihedral : 4.050 47.090 1955 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.13 % Allowed : 15.38 % Favored : 83.48 % 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: 0.90 (0.20), residues: 1786 helix: 1.69 (0.16), residues: 1100 sheet: 0.58 (0.48), residues: 111 loop : -1.61 (0.24), residues: 575 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 0.033 0.001 PHE B 492 TRP 0.006 0.001 TRP B 301 HIS 0.009 0.001 HIS C 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15184) covalent geometry : angle 0.55214 / 0.27 (20552) hydrogen bonds : bond 0.03387 / 2.28 ( 755) hydrogen bonds : angle 3.64093 / 2.53 ( 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 178 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 MET cc_start: 0.8378 (tpp) cc_final: 0.7896 (tpp) REVERT: B 288 LYS cc_start: 0.8122 (tppt) cc_final: 0.7808 (mtmm) REVERT: B 363 MET cc_start: 0.5950 (ppp) cc_final: 0.5585 (mtm) REVERT: B 562 ASP cc_start: 0.7329 (t0) cc_final: 0.7017 (t0) REVERT: C 32 LYS cc_start: 0.5543 (ptmt) cc_final: 0.5321 (tptt) REVERT: C 707 LEU cc_start: 0.8088 (mm) cc_final: 0.7830 (mt) REVERT: E 203 PHE cc_start: 0.7150 (t80) cc_final: 0.6921 (t80) outliers start: 19 outliers final: 17 residues processed: 176 average time/residue: 0.1148 time to fit residues: 31.1098 Evaluate side-chains 165 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 329 ILE 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 Chi-restraints excluded: chain E residue 396 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 100 optimal weight: 0.0570 chunk 162 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 126 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 = 0.3724 r_free = 0.3724 target = 0.132579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107987 restraints weight = 24108.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110916 restraints weight = 14717.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112870 restraints weight = 10582.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114106 restraints weight = 8490.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115068 restraints weight = 7365.285| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15184 Z= 0.101 Angle : 0.551 16.040 20552 Z= 0.273 Chirality : 0.038 0.159 2344 Planarity : 0.003 0.041 2591 Dihedral : 3.994 46.899 1955 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.01 % Allowed : 15.68 % 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: 0.97 (0.20), residues: 1786 helix: 1.74 (0.16), residues: 1100 sheet: 0.56 (0.48), residues: 114 loop : -1.58 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 786 TYR 0.023 0.001 TYR B 508 PHE 0.020 0.001 PHE C 372 TRP 0.005 0.001 TRP E 162 HIS 0.007 0.001 HIS C 591 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (15184) covalent geometry : angle 0.55084 / 0.27 (20552) hydrogen bonds : bond 0.03198 / 2.15 ( 755) hydrogen bonds : angle 3.59882 / 2.50 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.05 seconds wall clock time: 36 minutes 53.76 seconds (2213.76 seconds total)