Starting phenix.real_space_refine on Fri Feb 6 19:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6p_63916/02_2026/9u6p_63916.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 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 7 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 17124 2.51 5 N 4648 2.21 5 O 5095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26978 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3683 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1620 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.09, per 1000 atoms: 0.23 Number of scatterers: 26978 At special positions: 0 Unit cell: (139.24, 141.6, 160.48, 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 101 16.00 P 7 15.00 Mg 3 11.99 O 5095 8.00 N 4648 7.00 C 17124 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 25 sheets defined 44.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.869A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.158A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.154A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.527A pdb=" N ALA A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.513A pdb=" N ARG A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.637A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.671A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.471A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.668A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 removed outlier: 3.524A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.519A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.849A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.606A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.684A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.132A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 327 through 341 removed outlier: 3.723A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix removed outlier: 3.901A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 464 removed outlier: 3.981A pdb=" N ASP B 452 " --> pdb=" O PRO B 448 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 4.424A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.726A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.603A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.782A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.708A pdb=" N GLU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.021A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.122A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.598A pdb=" N ARG C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.506A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 415 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.702A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.075A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 531 removed outlier: 3.821A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.601A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.981A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 577 removed outlier: 3.784A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.837A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.661A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.573A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix removed outlier: 3.526A pdb=" N ALA D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.801A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.714A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.932A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.566A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.928A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 4.389A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.580A pdb=" N GLU D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.957A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.518A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.903A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 removed outlier: 3.811A pdb=" N SER E 215 " --> pdb=" O GLY E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.909A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.930A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.808A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.757A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.738A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 removed outlier: 3.880A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.672A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.613A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.893A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.105A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.968A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 331 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.618A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.057A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.592A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.599A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 467 through 472 removed outlier: 4.073A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 72 removed outlier: 3.682A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 120 through 167 removed outlier: 4.006A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 206 removed outlier: 3.516A pdb=" N GLN G 175 " --> pdb=" O GLY G 171 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN G 181 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.539A pdb=" N ALA H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.848A pdb=" N GLU H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.731A pdb=" N VAL H 59 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 4.052A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 removed outlier: 3.517A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.703A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 6.602A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.063A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.718A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 50 removed outlier: 6.598A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.654A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.711A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.611A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.631A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.920A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 7.045A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.547A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 7.000A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.473A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.753A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.537A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 352 through 359 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.710A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.536A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 89 through 96 removed outlier: 3.829A pdb=" N GLU G 92 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.421A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 2925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 3.04 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: 9015 1.34 - 1.46: 3696 1.46 - 1.57: 14595 1.57 - 1.69: 9 1.69 - 1.81: 190 Bond restraints: 27505 Sorted by residual: bond pdb=" O3 PO4 B 603 " pdb=" P PO4 B 603 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" O2 PO4 B 603 " pdb=" P PO4 B 603 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.58e+00 bond pdb=" O4 PO4 B 603 " pdb=" P PO4 B 603 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.24e+00 bond pdb=" C LEU H 68 " pdb=" N PRO H 69 " ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 9.14e+00 bond pdb=" O1 PO4 B 603 " pdb=" P PO4 B 603 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 7.99e+00 ... (remaining 27500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 36657 1.93 - 3.85: 551 3.85 - 5.78: 57 5.78 - 7.70: 20 7.70 - 9.63: 1 Bond angle restraints: 37286 Sorted by residual: angle pdb=" N GLY H 99 " pdb=" CA GLY H 99 " pdb=" C GLY H 99 " ideal model delta sigma weight residual 115.42 120.55 -5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" N LYS D 370 " pdb=" CA LYS D 370 " pdb=" C LYS D 370 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" N THR D 258 " pdb=" CA THR D 258 " pdb=" C THR D 258 " ideal model delta sigma weight residual 111.36 114.46 -3.10 1.09e+00 8.42e-01 8.07e+00 angle pdb=" N VAL B 503 " pdb=" CA VAL B 503 " pdb=" C VAL B 503 " ideal model delta sigma weight residual 113.53 110.78 2.75 9.80e-01 1.04e+00 7.85e+00 angle pdb=" N THR E 258 " pdb=" CA THR E 258 " pdb=" C THR E 258 " ideal model delta sigma weight residual 111.28 114.30 -3.02 1.09e+00 8.42e-01 7.67e+00 ... (remaining 37281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.58: 15415 19.58 - 39.16: 1004 39.16 - 58.74: 195 58.74 - 78.32: 53 78.32 - 97.90: 25 Dihedral angle restraints: 16692 sinusoidal: 6843 harmonic: 9849 Sorted by residual: dihedral pdb=" O1B ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PB ADP B 602 " pdb=" PA ADP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 -157.90 97.90 1 2.00e+01 2.50e-03 2.73e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 31.73 -91.73 1 2.00e+01 2.50e-03 2.47e+01 dihedral pdb=" CA PHE C 415 " pdb=" C PHE C 415 " pdb=" N ARG C 416 " pdb=" CA ARG C 416 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 16689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3186 0.051 - 0.102: 772 0.102 - 0.152: 199 0.152 - 0.203: 1 0.203 - 0.254: 3 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4158 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO E 324 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 294 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO C 295 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO F 324 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.026 5.00e-02 4.00e+02 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 7 2.26 - 2.92: 10503 2.92 - 3.58: 36406 3.58 - 4.24: 59767 4.24 - 4.90: 105234 Nonbonded interactions: 211917 Sorted by model distance: nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 601 " model vdw 1.600 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1B ADP C 602 " model vdw 1.992 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.025 2.170 nonbonded pdb=" OG1 THR C 235 " pdb="MG MG C 601 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.078 2.170 ... (remaining 211912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 602) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.060 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27505 Z= 0.170 Angle : 0.606 9.629 37286 Z= 0.339 Chirality : 0.046 0.254 4161 Planarity : 0.005 0.052 4874 Dihedral : 14.297 97.901 10414 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.84 % Allowed : 6.47 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.21 (0.14), residues: 3437 helix: 0.43 (0.14), residues: 1264 sheet: 0.44 (0.22), residues: 568 loop : -0.07 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 32 TYR 0.018 0.001 TYR F 54 PHE 0.013 0.001 PHE A 230 TRP 0.010 0.001 TRP A 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00372 (27505) covalent geometry : angle 0.60593 (37286) hydrogen bonds : bond 0.20375 ( 1027) hydrogen bonds : angle 6.59604 ( 2925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 473 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 MET cc_start: 0.8968 (mtp) cc_final: 0.8542 (mtp) REVERT: B 130 ARG cc_start: 0.7360 (mmp-170) cc_final: 0.7059 (mmp-170) REVERT: B 262 MET cc_start: 0.8839 (tpp) cc_final: 0.8386 (mmp) REVERT: B 282 MET cc_start: 0.9104 (mmm) cc_final: 0.8799 (mmm) REVERT: B 348 GLU cc_start: 0.7435 (pt0) cc_final: 0.7192 (pt0) REVERT: B 449 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: B 461 GLU cc_start: 0.7725 (tt0) cc_final: 0.7430 (tt0) REVERT: C 264 ASP cc_start: 0.7989 (t0) cc_final: 0.7783 (t0) REVERT: C 268 GLU cc_start: 0.7602 (pt0) cc_final: 0.7392 (pt0) REVERT: C 481 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8224 (ttm110) REVERT: C 539 ILE cc_start: 0.9087 (mt) cc_final: 0.8871 (mm) REVERT: C 567 MET cc_start: 0.9296 (mmm) cc_final: 0.9043 (mmm) REVERT: D 178 SER cc_start: 0.8396 (t) cc_final: 0.8142 (p) REVERT: D 260 MET cc_start: 0.8331 (mmm) cc_final: 0.7997 (mmm) REVERT: D 269 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 320 ASP cc_start: 0.8441 (t0) cc_final: 0.8095 (t0) REVERT: D 420 ARG cc_start: 0.8409 (ttm170) cc_final: 0.7995 (mtm-85) REVERT: D 465 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7652 (tm-30) REVERT: E 239 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8616 (mm) REVERT: E 368 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7561 (mmpt) REVERT: F 7 GLU cc_start: 0.4086 (pm20) cc_final: 0.2315 (pt0) REVERT: F 318 ASP cc_start: 0.8807 (t70) cc_final: 0.8552 (t70) REVERT: G 47 MET cc_start: 0.8393 (ttp) cc_final: 0.8134 (ttm) REVERT: G 133 TYR cc_start: 0.7895 (t80) cc_final: 0.7694 (t80) REVERT: G 149 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8173 (ttmt) REVERT: G 156 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8892 (tmtt) REVERT: G 205 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7624 (pp20) REVERT: H 11 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: H 19 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7122 (mp0) REVERT: H 35 THR cc_start: 0.8361 (m) cc_final: 0.8153 (p) REVERT: H 47 VAL cc_start: 0.8848 (t) cc_final: 0.8362 (p) REVERT: H 69 PRO cc_start: 0.7043 (Cg_exo) cc_final: 0.6779 (Cg_endo) REVERT: H 74 ILE cc_start: 0.7972 (pt) cc_final: 0.7729 (pp) REVERT: H 89 TYR cc_start: 0.8321 (t80) cc_final: 0.8080 (t80) outliers start: 52 outliers final: 10 residues processed: 516 average time/residue: 0.7940 time to fit residues: 465.0672 Evaluate side-chains 299 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 286 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 11 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 ASN B 477 GLN D 424 ASN F 161 ASN F 206 GLN F 310 GLN F 448 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.099120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.075958 restraints weight = 49305.329| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.76 r_work: 0.2862 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27505 Z= 0.120 Angle : 0.555 9.415 37286 Z= 0.281 Chirality : 0.043 0.162 4161 Planarity : 0.005 0.064 4874 Dihedral : 5.941 89.530 3872 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.33 % Allowed : 12.09 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.75 (0.14), residues: 3437 helix: 1.05 (0.15), residues: 1312 sheet: 0.55 (0.22), residues: 559 loop : 0.14 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 154 TYR 0.017 0.001 TYR D 349 PHE 0.016 0.001 PHE C 415 TRP 0.012 0.001 TRP A 119 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00262 (27505) covalent geometry : angle 0.55456 (37286) hydrogen bonds : bond 0.04920 ( 1027) hydrogen bonds : angle 4.77485 ( 2925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8802 (mtp) REVERT: A 332 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 79 MET cc_start: 0.9100 (mtp) cc_final: 0.8748 (mtp) REVERT: B 209 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: B 262 MET cc_start: 0.8530 (tpp) cc_final: 0.8308 (mmp) REVERT: B 282 MET cc_start: 0.9092 (mmm) cc_final: 0.8669 (mmm) REVERT: B 449 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7921 (pm20) REVERT: B 461 GLU cc_start: 0.7668 (tt0) cc_final: 0.7270 (tt0) REVERT: C 133 MET cc_start: 0.8674 (mtm) cc_final: 0.8410 (mtm) REVERT: C 264 ASP cc_start: 0.8151 (t0) cc_final: 0.7808 (t0) REVERT: C 268 GLU cc_start: 0.7750 (pt0) cc_final: 0.7387 (pt0) REVERT: C 287 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7827 (tp) REVERT: C 442 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7329 (m-40) REVERT: C 481 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8010 (ttm110) REVERT: C 493 ASP cc_start: 0.8442 (t0) cc_final: 0.7025 (m-30) REVERT: C 567 MET cc_start: 0.8904 (mmm) cc_final: 0.8566 (mmm) REVERT: D 178 SER cc_start: 0.8462 (t) cc_final: 0.7860 (p) REVERT: D 200 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7180 (mt-10) REVERT: D 269 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 320 ASP cc_start: 0.8206 (t0) cc_final: 0.7794 (t0) REVERT: D 420 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8169 (mmt90) REVERT: D 465 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7187 (tm-30) REVERT: E 141 MET cc_start: 0.8604 (mtp) cc_final: 0.8195 (mtp) REVERT: E 368 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7455 (mmpt) REVERT: E 420 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8457 (ttm170) REVERT: E 467 LEU cc_start: 0.6638 (mp) cc_final: 0.6206 (tm) REVERT: F 7 GLU cc_start: 0.3412 (pm20) cc_final: 0.2359 (pm20) REVERT: F 318 ASP cc_start: 0.8885 (t70) cc_final: 0.8684 (t70) REVERT: F 465 GLN cc_start: 0.7977 (tp40) cc_final: 0.7564 (tp-100) REVERT: G 47 MET cc_start: 0.8433 (ttp) cc_final: 0.8214 (ttm) REVERT: G 108 PHE cc_start: 0.3970 (t80) cc_final: 0.2091 (t80) REVERT: G 149 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7541 (ttmt) REVERT: G 156 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8492 (tmtt) REVERT: G 205 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7916 (tm-30) REVERT: H 11 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: H 47 VAL cc_start: 0.8172 (t) cc_final: 0.7636 (p) REVERT: H 63 MET cc_start: 0.6050 (mmm) cc_final: 0.5832 (mmp) REVERT: H 66 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6990 (ttm170) REVERT: H 74 ILE cc_start: 0.7622 (pt) cc_final: 0.7398 (pp) REVERT: H 95 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7966 (mmm160) outliers start: 66 outliers final: 22 residues processed: 355 average time/residue: 0.7171 time to fit residues: 291.8414 Evaluate side-chains 310 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 420 ARG Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 240 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 149 optimal weight: 0.0770 chunk 188 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 HIS B 477 GLN D 424 ASN F 23 ASN F 166 GLN F 170 GLN F 206 GLN F 448 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.071437 restraints weight = 50207.667| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.81 r_work: 0.2793 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 27505 Z= 0.238 Angle : 0.656 12.060 37286 Z= 0.334 Chirality : 0.048 0.195 4161 Planarity : 0.006 0.073 4874 Dihedral : 6.190 103.506 3866 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.64 % Allowed : 12.55 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.14), residues: 3437 helix: 1.11 (0.15), residues: 1312 sheet: 0.24 (0.23), residues: 547 loop : -0.08 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 409 TYR 0.031 0.002 TYR F 54 PHE 0.025 0.002 PHE C 415 TRP 0.015 0.001 TRP A 119 HIS 0.007 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00578 (27505) covalent geometry : angle 0.65570 (37286) hydrogen bonds : bond 0.06336 ( 1027) hydrogen bonds : angle 4.78980 ( 2925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 295 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8588 (t0) cc_final: 0.8365 (t70) REVERT: A 130 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7442 (ttm110) REVERT: A 209 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7896 (mmm) REVERT: A 332 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7903 (mt-10) REVERT: A 461 GLU cc_start: 0.8735 (tt0) cc_final: 0.8466 (tt0) REVERT: A 468 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8793 (p) REVERT: A 493 ASP cc_start: 0.8493 (t0) cc_final: 0.8237 (t0) REVERT: A 568 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8178 (mmtp) REVERT: B 54 ASP cc_start: 0.8538 (t0) cc_final: 0.8072 (p0) REVERT: B 79 MET cc_start: 0.9189 (mtp) cc_final: 0.8899 (mtp) REVERT: B 130 ARG cc_start: 0.7567 (mmp-170) cc_final: 0.7183 (mmm160) REVERT: B 209 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8224 (mtp) REVERT: B 336 GLU cc_start: 0.8567 (tt0) cc_final: 0.8309 (tm-30) REVERT: B 348 GLU cc_start: 0.8348 (pt0) cc_final: 0.7888 (pt0) REVERT: B 449 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 577 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7847 (mm) REVERT: C 268 GLU cc_start: 0.8093 (pt0) cc_final: 0.7819 (pt0) REVERT: C 294 MET cc_start: 0.8342 (mtt) cc_final: 0.7972 (mtt) REVERT: C 323 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8391 (mmt) REVERT: C 336 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8287 (tp30) REVERT: C 363 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8726 (mm-30) REVERT: C 441 GLU cc_start: 0.8646 (pp20) cc_final: 0.8145 (pp20) REVERT: C 442 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8232 (m-40) REVERT: C 481 ARG cc_start: 0.8401 (mmm160) cc_final: 0.8074 (ttp-110) REVERT: C 567 MET cc_start: 0.8787 (mmm) cc_final: 0.8586 (mmm) REVERT: D 178 SER cc_start: 0.8668 (t) cc_final: 0.8237 (p) REVERT: D 200 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 209 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: D 260 MET cc_start: 0.8532 (mmm) cc_final: 0.8147 (mmm) REVERT: D 269 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 320 ASP cc_start: 0.8520 (t0) cc_final: 0.8196 (t0) REVERT: D 420 ARG cc_start: 0.8367 (ttm170) cc_final: 0.7927 (mmt90) REVERT: D 465 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7701 (tp40) REVERT: E 141 MET cc_start: 0.8705 (mtp) cc_final: 0.8383 (mtp) REVERT: E 162 GLU cc_start: 0.8379 (mp0) cc_final: 0.8122 (mp0) REVERT: E 265 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8141 (mm-30) REVERT: E 318 ASP cc_start: 0.8675 (t0) cc_final: 0.8395 (t0) REVERT: E 368 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7965 (mmpt) REVERT: F 7 GLU cc_start: 0.4261 (pm20) cc_final: 0.2589 (pt0) REVERT: F 34 ASP cc_start: 0.8478 (m-30) cc_final: 0.8170 (m-30) REVERT: F 37 ASP cc_start: 0.8197 (t0) cc_final: 0.7910 (t0) REVERT: F 200 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: F 206 GLN cc_start: 0.8109 (mt0) cc_final: 0.7857 (mp10) REVERT: F 230 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8394 (mt-10) REVERT: F 318 ASP cc_start: 0.9039 (t70) cc_final: 0.8728 (t70) REVERT: F 465 GLN cc_start: 0.8057 (tp40) cc_final: 0.7689 (tp40) REVERT: G 17 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: G 108 PHE cc_start: 0.3950 (t80) cc_final: 0.3677 (t80) REVERT: G 149 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7841 (ttmt) REVERT: G 156 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8642 (tmtt) REVERT: G 205 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7949 (tm-30) REVERT: H 11 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: H 39 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6381 (mmm-85) REVERT: H 47 VAL cc_start: 0.8209 (t) cc_final: 0.7553 (p) REVERT: H 59 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7472 (p) REVERT: H 74 ILE cc_start: 0.7750 (pt) cc_final: 0.7491 (pp) REVERT: H 95 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8023 (mmm160) outliers start: 103 outliers final: 30 residues processed: 362 average time/residue: 0.7872 time to fit residues: 324.4159 Evaluate side-chains 304 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 229 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 307 optimal weight: 0.6980 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN F 448 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073432 restraints weight = 49985.839| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.81 r_work: 0.2822 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27505 Z= 0.125 Angle : 0.535 8.957 37286 Z= 0.267 Chirality : 0.044 0.154 4161 Planarity : 0.004 0.057 4874 Dihedral : 5.730 95.288 3862 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.83 % Allowed : 14.32 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.88 (0.15), residues: 3437 helix: 1.50 (0.15), residues: 1296 sheet: 0.36 (0.23), residues: 529 loop : -0.00 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 130 TYR 0.016 0.001 TYR F 54 PHE 0.019 0.001 PHE C 415 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00291 (27505) covalent geometry : angle 0.53461 (37286) hydrogen bonds : bond 0.04811 ( 1027) hydrogen bonds : angle 4.53687 ( 2925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 269 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (mmm) REVERT: A 332 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 538 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8606 (tp30) REVERT: A 568 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8004 (mmtp) REVERT: B 79 MET cc_start: 0.9184 (mtp) cc_final: 0.8969 (mtp) REVERT: B 130 ARG cc_start: 0.7518 (mmp-170) cc_final: 0.7061 (mmp-170) REVERT: B 323 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8437 (mmt) REVERT: B 325 ASP cc_start: 0.8513 (t70) cc_final: 0.8308 (t70) REVERT: B 336 GLU cc_start: 0.8522 (tt0) cc_final: 0.8268 (tm-30) REVERT: B 348 GLU cc_start: 0.8301 (pt0) cc_final: 0.7818 (pt0) REVERT: B 446 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8306 (p0) REVERT: C 130 ARG cc_start: 0.8592 (ttm110) cc_final: 0.7908 (ttm110) REVERT: C 133 MET cc_start: 0.8751 (mtm) cc_final: 0.8538 (mtp) REVERT: C 323 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8397 (mmt) REVERT: C 336 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8284 (tp30) REVERT: C 363 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 390 ASP cc_start: 0.8818 (t0) cc_final: 0.8604 (m-30) REVERT: C 442 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8251 (m-40) REVERT: C 461 GLU cc_start: 0.8049 (tt0) cc_final: 0.7812 (tm-30) REVERT: C 567 MET cc_start: 0.8735 (mmm) cc_final: 0.8502 (mmm) REVERT: D 178 SER cc_start: 0.8646 (t) cc_final: 0.8129 (p) REVERT: D 200 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 269 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 320 ASP cc_start: 0.8432 (t0) cc_final: 0.8123 (t0) REVERT: D 321 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8214 (tmt170) REVERT: D 465 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7781 (tp-100) REVERT: E 98 LYS cc_start: 0.9067 (mppt) cc_final: 0.8863 (mmmt) REVERT: E 141 MET cc_start: 0.8694 (mtp) cc_final: 0.8216 (mtp) REVERT: E 265 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 318 ASP cc_start: 0.8704 (t0) cc_final: 0.8402 (t0) REVERT: E 334 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8788 (mm-30) REVERT: E 362 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.9005 (ttm) REVERT: E 368 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7953 (mmpt) REVERT: F 7 GLU cc_start: 0.4338 (pm20) cc_final: 0.3360 (pm20) REVERT: F 37 ASP cc_start: 0.8201 (t0) cc_final: 0.7924 (t0) REVERT: F 206 GLN cc_start: 0.8148 (mt0) cc_final: 0.7887 (mp10) REVERT: F 230 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8364 (mt-10) REVERT: F 318 ASP cc_start: 0.8928 (t70) cc_final: 0.8652 (t70) REVERT: F 334 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8841 (mp0) REVERT: F 465 GLN cc_start: 0.7925 (tp40) cc_final: 0.7430 (tp40) REVERT: G 17 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: G 108 PHE cc_start: 0.4037 (t80) cc_final: 0.3799 (t80) REVERT: G 149 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7864 (ttmt) REVERT: G 156 LYS cc_start: 0.9148 (ttpt) cc_final: 0.8663 (tmtt) REVERT: G 205 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7961 (tm-30) REVERT: H 11 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: H 21 TYR cc_start: 0.7282 (m-10) cc_final: 0.7054 (m-10) REVERT: H 59 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7465 (p) REVERT: H 74 ILE cc_start: 0.7766 (pt) cc_final: 0.7513 (pp) REVERT: H 95 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8125 (mmm160) REVERT: H 103 LYS cc_start: 0.7790 (tmtm) cc_final: 0.7556 (tmtm) outliers start: 80 outliers final: 27 residues processed: 321 average time/residue: 0.8365 time to fit residues: 305.4124 Evaluate side-chains 290 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 304 optimal weight: 0.0470 chunk 197 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 329 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN F 448 GLN G 10 ASN G 13 GLN H 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073649 restraints weight = 49709.927| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.78 r_work: 0.2834 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27505 Z= 0.118 Angle : 0.526 9.693 37286 Z= 0.261 Chirality : 0.043 0.154 4161 Planarity : 0.004 0.064 4874 Dihedral : 5.344 90.808 3859 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.93 % Allowed : 14.63 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.06 (0.15), residues: 3437 helix: 1.69 (0.15), residues: 1301 sheet: 0.47 (0.23), residues: 537 loop : 0.04 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 154 TYR 0.011 0.001 TYR F 54 PHE 0.014 0.001 PHE C 415 TRP 0.010 0.001 TRP B 119 HIS 0.002 0.000 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00277 (27505) covalent geometry : angle 0.52559 (37286) hydrogen bonds : bond 0.04400 ( 1027) hydrogen bonds : angle 4.38549 ( 2925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 261 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7664 (ttm-80) REVERT: A 209 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: A 332 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 466 GLU cc_start: 0.8550 (pp20) cc_final: 0.8071 (pp20) REVERT: A 538 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8544 (tp30) REVERT: A 568 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8003 (mmtp) REVERT: B 79 MET cc_start: 0.9137 (mtp) cc_final: 0.8894 (mtp) REVERT: B 130 ARG cc_start: 0.7515 (mmp-170) cc_final: 0.7219 (mmp-170) REVERT: B 323 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8391 (mmt) REVERT: B 325 ASP cc_start: 0.8516 (t70) cc_final: 0.8209 (t70) REVERT: B 336 GLU cc_start: 0.8542 (tt0) cc_final: 0.8316 (tm-30) REVERT: B 348 GLU cc_start: 0.8314 (pt0) cc_final: 0.7821 (pt0) REVERT: B 456 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8263 (pp20) REVERT: C 133 MET cc_start: 0.8703 (mtm) cc_final: 0.8466 (mtp) REVERT: C 323 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8377 (mmt) REVERT: C 336 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8317 (tp30) REVERT: C 390 ASP cc_start: 0.8828 (t0) cc_final: 0.8593 (m-30) REVERT: C 393 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: C 442 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8112 (m-40) REVERT: C 461 GLU cc_start: 0.7988 (tt0) cc_final: 0.7759 (tt0) REVERT: C 567 MET cc_start: 0.8683 (mmm) cc_final: 0.8452 (mmm) REVERT: D 178 SER cc_start: 0.8633 (t) cc_final: 0.8134 (p) REVERT: D 200 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 260 MET cc_start: 0.8473 (mmm) cc_final: 0.7938 (mmm) REVERT: D 320 ASP cc_start: 0.8397 (t0) cc_final: 0.8152 (t0) REVERT: D 321 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8207 (tmt170) REVERT: D 465 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7486 (tm-30) REVERT: E 98 LYS cc_start: 0.9095 (mppt) cc_final: 0.8890 (mmmt) REVERT: E 141 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: E 162 GLU cc_start: 0.8445 (mp0) cc_final: 0.8203 (mp0) REVERT: E 265 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7935 (mm-30) REVERT: E 318 ASP cc_start: 0.8705 (t0) cc_final: 0.8396 (t0) REVERT: E 334 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8767 (mm-30) REVERT: E 368 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7911 (mmpt) REVERT: F 7 GLU cc_start: 0.3827 (pm20) cc_final: 0.2596 (pm20) REVERT: F 34 ASP cc_start: 0.8374 (m-30) cc_final: 0.8028 (m-30) REVERT: F 206 GLN cc_start: 0.8109 (mt0) cc_final: 0.7894 (mp10) REVERT: F 318 ASP cc_start: 0.8910 (t70) cc_final: 0.8638 (t70) REVERT: F 465 GLN cc_start: 0.7867 (tp40) cc_final: 0.7559 (tp40) REVERT: G 17 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: G 156 LYS cc_start: 0.9134 (ttpt) cc_final: 0.8720 (ttpt) REVERT: G 205 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7939 (tm-30) REVERT: H 39 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6313 (mmm-85) REVERT: H 47 VAL cc_start: 0.8210 (t) cc_final: 0.7541 (p) REVERT: H 59 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7638 (p) REVERT: H 74 ILE cc_start: 0.7773 (pt) cc_final: 0.7517 (pp) REVERT: H 95 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8126 (mmm160) outliers start: 83 outliers final: 33 residues processed: 316 average time/residue: 0.7843 time to fit residues: 283.4694 Evaluate side-chains 296 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 271 optimal weight: 8.9990 chunk 230 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 150 optimal weight: 0.0010 chunk 16 optimal weight: 8.9990 chunk 198 optimal weight: 0.4980 chunk 241 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 166 GLN F 448 GLN G 10 ASN G 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076785 restraints weight = 48112.118| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.75 r_work: 0.2898 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27505 Z= 0.095 Angle : 0.513 9.138 37286 Z= 0.253 Chirality : 0.042 0.213 4161 Planarity : 0.004 0.047 4874 Dihedral : 5.061 85.186 3856 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.62 % Allowed : 15.31 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.29 (0.15), residues: 3437 helix: 1.85 (0.15), residues: 1306 sheet: 0.55 (0.22), residues: 576 loop : 0.22 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 401 TYR 0.009 0.001 TYR E 13 PHE 0.010 0.001 PHE C 415 TRP 0.009 0.001 TRP B 119 HIS 0.002 0.000 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00209 (27505) covalent geometry : angle 0.51300 (37286) hydrogen bonds : bond 0.03817 ( 1027) hydrogen bonds : angle 4.25096 ( 2925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: A 332 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 343 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: A 491 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8309 (mtm-85) REVERT: A 538 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: B 130 ARG cc_start: 0.7491 (mmp-170) cc_final: 0.7168 (mmp-170) REVERT: B 325 ASP cc_start: 0.8515 (t70) cc_final: 0.8250 (t70) REVERT: B 348 GLU cc_start: 0.8234 (pt0) cc_final: 0.7757 (pt0) REVERT: B 446 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8204 (p0) REVERT: B 456 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8276 (pp20) REVERT: C 336 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8419 (tp30) REVERT: C 390 ASP cc_start: 0.8827 (t0) cc_final: 0.8574 (m-30) REVERT: C 393 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7259 (pp20) REVERT: C 442 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: C 567 MET cc_start: 0.8720 (mmm) cc_final: 0.8476 (mmm) REVERT: D 178 SER cc_start: 0.8616 (t) cc_final: 0.8121 (p) REVERT: D 200 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7582 (mt-10) REVERT: D 260 MET cc_start: 0.8625 (mmm) cc_final: 0.8093 (mmm) REVERT: D 321 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8252 (tmt170) REVERT: D 376 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6937 (mmtt) REVERT: D 465 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7440 (tm-30) REVERT: E 141 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: E 162 GLU cc_start: 0.8514 (mp0) cc_final: 0.8277 (mp0) REVERT: E 239 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8864 (mm) REVERT: E 318 ASP cc_start: 0.8600 (t0) cc_final: 0.8341 (t0) REVERT: E 368 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7856 (mmpt) REVERT: E 413 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7951 (tm-30) REVERT: F 7 GLU cc_start: 0.4187 (pm20) cc_final: 0.3081 (pm20) REVERT: F 318 ASP cc_start: 0.8889 (t70) cc_final: 0.8593 (t70) REVERT: F 334 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: F 465 GLN cc_start: 0.7924 (tp40) cc_final: 0.7645 (tp40) REVERT: G 17 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8034 (mp10) REVERT: G 205 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8037 (tm-30) REVERT: H 1 MET cc_start: 0.7546 (pmm) cc_final: 0.7242 (mpm) REVERT: H 39 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6217 (mmm-85) REVERT: H 47 VAL cc_start: 0.8362 (t) cc_final: 0.7687 (p) REVERT: H 59 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7608 (p) REVERT: H 74 ILE cc_start: 0.7877 (pt) cc_final: 0.7611 (pp) REVERT: H 95 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8070 (mmm160) outliers start: 74 outliers final: 23 residues processed: 311 average time/residue: 0.8308 time to fit residues: 294.1346 Evaluate side-chains 287 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 227 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 GLN G 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.075294 restraints weight = 48111.379| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.71 r_work: 0.2874 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27505 Z= 0.131 Angle : 0.535 9.025 37286 Z= 0.265 Chirality : 0.044 0.155 4161 Planarity : 0.004 0.072 4874 Dihedral : 5.077 86.610 3855 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.58 % Allowed : 15.73 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.25 (0.15), residues: 3437 helix: 1.83 (0.15), residues: 1310 sheet: 0.56 (0.23), residues: 557 loop : 0.16 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 154 TYR 0.016 0.001 TYR H 21 PHE 0.022 0.001 PHE C 415 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00314 (27505) covalent geometry : angle 0.53541 (37286) hydrogen bonds : bond 0.04234 ( 1027) hydrogen bonds : angle 4.25417 ( 2925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7631 (ttm-80) REVERT: A 209 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8205 (mmm) REVERT: A 323 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8571 (mmt) REVERT: A 332 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7984 (mt-10) REVERT: A 466 GLU cc_start: 0.8565 (pp20) cc_final: 0.8125 (pp20) REVERT: A 491 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8345 (mtm-85) REVERT: B 130 ARG cc_start: 0.7573 (mmp-170) cc_final: 0.7211 (mmp-170) REVERT: B 348 GLU cc_start: 0.8253 (pt0) cc_final: 0.7780 (pt0) REVERT: B 401 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8560 (ttm-80) REVERT: B 456 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: C 336 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8444 (tp30) REVERT: C 390 ASP cc_start: 0.8850 (t0) cc_final: 0.8604 (m-30) REVERT: C 393 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: C 442 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8234 (m-40) REVERT: C 567 MET cc_start: 0.8709 (mmm) cc_final: 0.8469 (mmm) REVERT: D 178 SER cc_start: 0.8638 (t) cc_final: 0.8232 (p) REVERT: D 200 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7586 (mt-10) REVERT: D 260 MET cc_start: 0.8727 (mmm) cc_final: 0.8146 (mmm) REVERT: D 376 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.7018 (mmtt) REVERT: D 465 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7788 (tp40) REVERT: E 162 GLU cc_start: 0.8532 (mp0) cc_final: 0.8283 (mp0) REVERT: E 239 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8905 (mm) REVERT: E 318 ASP cc_start: 0.8634 (t0) cc_final: 0.8380 (t0) REVERT: E 368 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7925 (mmpt) REVERT: E 413 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7945 (tm-30) REVERT: F 7 GLU cc_start: 0.4339 (pm20) cc_final: 0.3209 (pm20) REVERT: F 318 ASP cc_start: 0.8911 (t70) cc_final: 0.8604 (t70) REVERT: F 334 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: F 450 GLU cc_start: 0.8298 (mp0) cc_final: 0.7797 (mp0) REVERT: F 465 GLN cc_start: 0.7942 (tp40) cc_final: 0.7534 (tp-100) REVERT: G 17 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: G 160 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7868 (mtp180) REVERT: G 205 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8049 (tm-30) REVERT: H 1 MET cc_start: 0.7532 (pmm) cc_final: 0.7221 (mpm) REVERT: H 39 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6333 (mmm-85) REVERT: H 47 VAL cc_start: 0.8348 (t) cc_final: 0.7674 (p) REVERT: H 59 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7538 (p) REVERT: H 74 ILE cc_start: 0.7858 (pt) cc_final: 0.7584 (pp) REVERT: H 95 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8027 (mmm160) outliers start: 73 outliers final: 28 residues processed: 305 average time/residue: 0.8037 time to fit residues: 280.0215 Evaluate side-chains 288 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 97 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 311 optimal weight: 0.8980 chunk 319 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN F 448 GLN G 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.097566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073578 restraints weight = 48832.105| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.72 r_work: 0.2843 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27505 Z= 0.176 Angle : 0.573 12.485 37286 Z= 0.285 Chirality : 0.045 0.162 4161 Planarity : 0.005 0.073 4874 Dihedral : 5.240 90.980 3855 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.51 % Allowed : 16.26 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3437 helix: 1.78 (0.15), residues: 1306 sheet: 0.45 (0.23), residues: 527 loop : 0.07 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 154 TYR 0.010 0.001 TYR A 500 PHE 0.021 0.001 PHE C 415 TRP 0.012 0.001 TRP B 119 HIS 0.004 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00427 (27505) covalent geometry : angle 0.57341 (37286) hydrogen bonds : bond 0.04829 ( 1027) hydrogen bonds : angle 4.33966 ( 2925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 154 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7697 (ttm-80) REVERT: A 209 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (mmm) REVERT: A 323 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8582 (mmt) REVERT: A 332 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 538 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8600 (tp30) REVERT: B 130 ARG cc_start: 0.7602 (mmp-170) cc_final: 0.7182 (mmp-170) REVERT: B 348 GLU cc_start: 0.8290 (pt0) cc_final: 0.7844 (pt0) REVERT: B 425 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8637 (t0) REVERT: C 336 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8537 (tp30) REVERT: C 393 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7552 (pp20) REVERT: C 442 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8317 (m-40) REVERT: C 461 GLU cc_start: 0.8090 (tt0) cc_final: 0.7857 (tt0) REVERT: D 78 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7498 (p0) REVERT: D 178 SER cc_start: 0.8631 (t) cc_final: 0.8219 (p) REVERT: D 200 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 260 MET cc_start: 0.8711 (mmm) cc_final: 0.8111 (mmm) REVERT: D 316 MET cc_start: 0.8946 (mtp) cc_final: 0.8735 (mtp) REVERT: D 376 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7123 (mmtt) REVERT: D 465 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7809 (tp40) REVERT: E 162 GLU cc_start: 0.8546 (mp0) cc_final: 0.8256 (mp0) REVERT: E 239 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8888 (mm) REVERT: E 355 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8435 (mm) REVERT: E 368 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7929 (mmpt) REVERT: E 413 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7941 (tm-30) REVERT: F 7 GLU cc_start: 0.3986 (pm20) cc_final: 0.2981 (pm20) REVERT: F 318 ASP cc_start: 0.8944 (t70) cc_final: 0.8634 (t70) REVERT: F 334 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: F 465 GLN cc_start: 0.7966 (tp40) cc_final: 0.7568 (tp-100) REVERT: G 17 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: G 160 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7852 (mtp180) REVERT: G 205 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8082 (tm-30) REVERT: H 1 MET cc_start: 0.7608 (pmm) cc_final: 0.7284 (mpm) REVERT: H 21 TYR cc_start: 0.6899 (m-10) cc_final: 0.6697 (m-10) REVERT: H 39 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6378 (mmm-85) REVERT: H 47 VAL cc_start: 0.8354 (t) cc_final: 0.7697 (p) REVERT: H 59 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7483 (p) REVERT: H 74 ILE cc_start: 0.7871 (pt) cc_final: 0.7595 (pp) REVERT: H 95 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8096 (mmm160) outliers start: 71 outliers final: 33 residues processed: 306 average time/residue: 0.7894 time to fit residues: 276.5170 Evaluate side-chains 294 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 54 TYR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 248 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 325 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 182 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 GLN ** H 30 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 = 0.3375 r_free = 0.3375 target = 0.098267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074266 restraints weight = 48539.527| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.72 r_work: 0.2853 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27505 Z= 0.145 Angle : 0.565 8.910 37286 Z= 0.283 Chirality : 0.044 0.159 4161 Planarity : 0.004 0.079 4874 Dihedral : 5.175 88.735 3855 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.09 % Allowed : 16.83 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.16 (0.15), residues: 3437 helix: 1.83 (0.15), residues: 1304 sheet: 0.44 (0.23), residues: 556 loop : 0.07 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 130 TYR 0.011 0.001 TYR A 500 PHE 0.016 0.001 PHE C 415 TRP 0.011 0.001 TRP B 119 HIS 0.003 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00348 (27505) covalent geometry : angle 0.56545 (37286) hydrogen bonds : bond 0.04497 ( 1027) hydrogen bonds : angle 4.29098 ( 2925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8486 (mtp) cc_final: 0.8285 (mmm) REVERT: A 154 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7702 (ttm-80) REVERT: A 209 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (mmm) REVERT: A 323 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8535 (mmt) REVERT: A 332 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 466 GLU cc_start: 0.8526 (pp20) cc_final: 0.8123 (pp20) REVERT: A 491 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8302 (mtm-85) REVERT: A 538 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (tp30) REVERT: B 130 ARG cc_start: 0.7540 (mmp-170) cc_final: 0.7136 (mmp-170) REVERT: B 348 GLU cc_start: 0.8293 (pt0) cc_final: 0.7864 (pt0) REVERT: B 393 GLU cc_start: 0.7901 (tt0) cc_final: 0.7577 (tm-30) REVERT: B 425 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8638 (t0) REVERT: B 456 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8272 (pp20) REVERT: C 336 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8567 (tp30) REVERT: C 347 GLU cc_start: 0.8078 (tp30) cc_final: 0.7875 (mt-10) REVERT: C 393 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: C 442 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8314 (m-40) REVERT: D 178 SER cc_start: 0.8625 (t) cc_final: 0.8109 (p) REVERT: D 200 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 260 MET cc_start: 0.8752 (mmm) cc_final: 0.8187 (mmm) REVERT: D 376 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7107 (mmtt) REVERT: D 465 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7821 (tp40) REVERT: E 162 GLU cc_start: 0.8588 (mp0) cc_final: 0.8297 (mp0) REVERT: E 239 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8900 (mm) REVERT: E 355 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8439 (mm) REVERT: E 368 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7939 (mmpt) REVERT: E 413 GLN cc_start: 0.8533 (mm-40) cc_final: 0.7935 (tm-30) REVERT: F 7 GLU cc_start: 0.4169 (pm20) cc_final: 0.3111 (pm20) REVERT: F 318 ASP cc_start: 0.8910 (t70) cc_final: 0.8586 (t70) REVERT: F 334 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: F 450 GLU cc_start: 0.8326 (mp0) cc_final: 0.8117 (mp0) REVERT: F 465 GLN cc_start: 0.7976 (tp40) cc_final: 0.7570 (tp-100) REVERT: G 17 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: G 160 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7873 (mtp180) REVERT: G 205 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8065 (tm-30) REVERT: H 1 MET cc_start: 0.7587 (pmm) cc_final: 0.7279 (mpm) REVERT: H 47 VAL cc_start: 0.8305 (t) cc_final: 0.7645 (p) REVERT: H 59 VAL cc_start: 0.7741 (OUTLIER) cc_final: 0.7487 (p) REVERT: H 74 ILE cc_start: 0.7859 (pt) cc_final: 0.7598 (pp) REVERT: H 95 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7942 (mmm160) outliers start: 59 outliers final: 30 residues processed: 288 average time/residue: 0.8302 time to fit residues: 272.2086 Evaluate side-chains 284 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 122 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 250 optimal weight: 0.6980 chunk 125 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 GLN ** H 30 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 = 0.3361 r_free = 0.3361 target = 0.097358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.073324 restraints weight = 48553.992| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.72 r_work: 0.2841 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27505 Z= 0.186 Angle : 0.590 12.377 37286 Z= 0.295 Chirality : 0.045 0.163 4161 Planarity : 0.005 0.086 4874 Dihedral : 5.248 91.231 3855 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 16.97 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.05 (0.15), residues: 3437 helix: 1.74 (0.15), residues: 1304 sheet: 0.36 (0.23), residues: 558 loop : 0.02 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 130 TYR 0.013 0.001 TYR A 500 PHE 0.015 0.001 PHE C 415 TRP 0.012 0.001 TRP B 119 HIS 0.003 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00452 (27505) covalent geometry : angle 0.58954 (37286) hydrogen bonds : bond 0.04832 ( 1027) hydrogen bonds : angle 4.34501 ( 2925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 122 MET cc_start: 0.8519 (mtp) cc_final: 0.8316 (mmm) REVERT: A 154 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7747 (ttm-80) REVERT: A 209 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8236 (mmm) REVERT: A 323 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8567 (mmt) REVERT: A 332 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8007 (mt-10) REVERT: A 466 GLU cc_start: 0.8562 (pp20) cc_final: 0.8124 (pp20) REVERT: A 491 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8298 (mtm-85) REVERT: A 538 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8641 (tp30) REVERT: B 130 ARG cc_start: 0.7557 (mmp-170) cc_final: 0.7181 (mmp-170) REVERT: B 348 GLU cc_start: 0.8309 (pt0) cc_final: 0.7887 (pt0) REVERT: B 393 GLU cc_start: 0.7910 (tt0) cc_final: 0.7580 (tm-30) REVERT: B 401 ARG cc_start: 0.8842 (ttm-80) cc_final: 0.8616 (ttm110) REVERT: B 425 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (t0) REVERT: B 456 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8294 (pp20) REVERT: C 336 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8482 (tp30) REVERT: C 393 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: C 442 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8327 (m-40) REVERT: D 53 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: D 78 ASP cc_start: 0.7765 (p0) cc_final: 0.7497 (p0) REVERT: D 178 SER cc_start: 0.8640 (t) cc_final: 0.8135 (p) REVERT: D 200 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7685 (mt-10) REVERT: D 260 MET cc_start: 0.8761 (mmm) cc_final: 0.8131 (mmm) REVERT: D 321 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8212 (tmt170) REVERT: D 376 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7151 (mmtt) REVERT: D 465 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7806 (tp40) REVERT: E 162 GLU cc_start: 0.8594 (mp0) cc_final: 0.8294 (mp0) REVERT: E 239 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8862 (mm) REVERT: E 318 ASP cc_start: 0.8717 (t70) cc_final: 0.8362 (t0) REVERT: E 355 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8442 (mm) REVERT: E 368 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7985 (mmpt) REVERT: E 395 LEU cc_start: 0.7726 (mt) cc_final: 0.7509 (tm) REVERT: F 7 GLU cc_start: 0.4036 (pm20) cc_final: 0.2879 (pm20) REVERT: F 37 ASP cc_start: 0.7765 (t0) cc_final: 0.7499 (t0) REVERT: F 206 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: F 318 ASP cc_start: 0.8906 (t70) cc_final: 0.8580 (t70) REVERT: F 334 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: G 17 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: G 160 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7892 (mtp180) REVERT: G 205 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8057 (tm-30) REVERT: H 1 MET cc_start: 0.7761 (pmm) cc_final: 0.7386 (mpm) REVERT: H 47 VAL cc_start: 0.8336 (t) cc_final: 0.7662 (p) REVERT: H 59 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7500 (p) REVERT: H 74 ILE cc_start: 0.7906 (pt) cc_final: 0.7638 (pp) REVERT: H 95 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8091 (mmm160) outliers start: 59 outliers final: 32 residues processed: 287 average time/residue: 0.8215 time to fit residues: 267.1607 Evaluate side-chains 286 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 321 ARG Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 376 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 160 ARG Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 1 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 GLN ** H 30 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 = 0.3363 r_free = 0.3363 target = 0.097545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073590 restraints weight = 48214.840| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.70 r_work: 0.2846 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27505 Z= 0.165 Angle : 0.577 10.490 37286 Z= 0.290 Chirality : 0.044 0.161 4161 Planarity : 0.005 0.088 4874 Dihedral : 5.246 90.766 3855 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.09 % Allowed : 16.93 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.05 (0.15), residues: 3437 helix: 1.76 (0.15), residues: 1304 sheet: 0.37 (0.23), residues: 557 loop : 0.01 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG C 130 TYR 0.013 0.001 TYR A 500 PHE 0.014 0.001 PHE C 415 TRP 0.012 0.001 TRP B 119 HIS 0.003 0.001 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00400 (27505) covalent geometry : angle 0.57744 (37286) hydrogen bonds : bond 0.04727 ( 1027) hydrogen bonds : angle 4.32830 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8728.59 seconds wall clock time: 149 minutes 21.78 seconds (8961.78 seconds total)