Starting phenix.real_space_refine on Sun Jul 5 00:42:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.map" model { file = "/net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ep0_28494/07_2026/8ep0_28494.cif" } resolution = 4.9 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= 0.004 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 15696 2.51 5 N 4108 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 246 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 142 Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 4.29, per 1000 atoms: 0.18 Number of scatterers: 24408 At special positions: 0 Unit cell: (169.56, 169.56, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4488 8.00 N 4108 7.00 C 15696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 65.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.059A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 4.114A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.057A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 269 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 4.094A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR C 347 " --> pdb=" O HIS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 473 removed outlier: 3.918A pdb=" N THR C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.876A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.996A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.846A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 242 Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 269 Processing helix chain 'D' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 4.566A pdb=" N TYR D 347 " --> pdb=" O HIS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 379 removed outlier: 3.649A pdb=" N LEU D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 418 through 435 Processing helix chain 'D' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY A 275 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL A 634 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 603 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE B 42 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 34 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 93 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY B 275 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL B 634 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 603 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.356A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.590A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 275 removed outlier: 4.898A pdb=" N GLY C 275 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL C 634 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN C 603 " --> pdb=" O VAL C 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE D 42 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN D 34 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 93 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY D 275 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL D 634 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN D 603 " --> pdb=" O VAL D 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4536 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: 4.29 Time building geometry restraints manager: 2.35 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: 7950 1.34 - 1.46: 4433 1.46 - 1.58: 12409 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 24964 Sorted by residual: bond pdb=" N PHE C 359 " pdb=" CA PHE C 359 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.17e-02 7.31e+03 4.25e+00 bond pdb=" N PHE B 359 " pdb=" CA PHE B 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.99e+00 bond pdb=" N PHE A 359 " pdb=" CA PHE A 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.97e+00 bond pdb=" N PHE D 359 " pdb=" CA PHE D 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.70e+00 bond pdb=" CD1 TYR B 428 " pdb=" CE1 TYR B 428 " ideal model delta sigma weight residual 1.382 1.324 0.058 3.00e-02 1.11e+03 3.70e+00 ... (remaining 24959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 32930 1.89 - 3.79: 1034 3.79 - 5.68: 164 5.68 - 7.57: 28 7.57 - 9.47: 8 Bond angle restraints: 34164 Sorted by residual: angle pdb=" N MET B 431 " pdb=" CA MET B 431 " pdb=" CB MET B 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.70e+01 angle pdb=" N MET D 431 " pdb=" CA MET D 431 " pdb=" CB MET D 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.69e+01 angle pdb=" N MET C 431 " pdb=" CA MET C 431 " pdb=" CB MET C 431 " ideal model delta sigma weight residual 110.01 102.52 7.49 1.45e+00 4.76e-01 2.67e+01 angle pdb=" N MET A 431 " pdb=" CA MET A 431 " pdb=" CB MET A 431 " ideal model delta sigma weight residual 110.01 102.53 7.48 1.45e+00 4.76e-01 2.66e+01 angle pdb=" C LYS B 450 " pdb=" CA LYS B 450 " pdb=" CB LYS B 450 " ideal model delta sigma weight residual 109.67 118.57 -8.90 2.01e+00 2.48e-01 1.96e+01 ... (remaining 34159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 13283 15.64 - 31.29: 966 31.29 - 46.93: 171 46.93 - 62.57: 32 62.57 - 78.21: 28 Dihedral angle restraints: 14480 sinusoidal: 4608 harmonic: 9872 Sorted by residual: dihedral pdb=" CA TYR D 499 " pdb=" C TYR D 499 " pdb=" N GLN D 500 " pdb=" CA GLN D 500 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A 499 " pdb=" C TYR A 499 " pdb=" N GLN A 500 " pdb=" CA GLN A 500 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR C 499 " pdb=" C TYR C 499 " pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3612 0.078 - 0.156: 348 0.156 - 0.234: 28 0.234 - 0.312: 10 0.312 - 0.389: 10 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CB ILE C 378 " pdb=" CA ILE C 378 " pdb=" CG1 ILE C 378 " pdb=" CG2 ILE C 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE D 378 " pdb=" CA ILE D 378 " pdb=" CG1 ILE D 378 " pdb=" CG2 ILE D 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 4005 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 47 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" CG ASP C 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP C 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 47 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CG ASP D 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP D 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP D 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 47 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" CG ASP A 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP A 47 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP A 47 " -0.023 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4831 2.77 - 3.30: 27126 3.30 - 3.83: 41904 3.83 - 4.37: 46091 4.37 - 4.90: 75741 Nonbonded interactions: 195693 Sorted by model distance: nonbonded pdb=" OG SER B 418 " pdb=" OD1 ASN B 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 418 " pdb=" OD1 ASN A 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 418 " pdb=" OD1 ASN C 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER D 418 " pdb=" OD1 ASN D 420 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 2.239 3.040 ... (remaining 195688 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.460 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.071 24964 Z= 0.196 Angle : 0.785 9.468 34164 Z= 0.454 Chirality : 0.051 0.389 4008 Planarity : 0.006 0.103 4416 Dihedral : 12.186 78.213 8080 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3340 helix: 0.25 (0.12), residues: 1928 sheet: 0.88 (0.36), residues: 172 loop : -0.21 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 84 TYR 0.040 0.003 TYR D 428 PHE 0.058 0.004 PHE B 17 TRP 0.030 0.003 TRP B 108 HIS 0.010 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (24964) covalent geometry : angle 0.78531 / 0.45 (34164) hydrogen bonds : bond 0.10439 / 7.12 ( 1572) hydrogen bonds : angle 5.44805 / 3.93 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9375 (tpp) cc_final: 0.9172 (tpp) REVERT: A 224 ILE cc_start: 0.9522 (pt) cc_final: 0.9233 (mm) REVERT: A 423 TYR cc_start: 0.8796 (t80) cc_final: 0.8402 (t80) REVERT: A 427 LEU cc_start: 0.9212 (tp) cc_final: 0.8877 (mt) REVERT: A 568 MET cc_start: 0.9272 (mmp) cc_final: 0.8953 (mmp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0512 time to fit residues: 5.9890 Evaluate side-chains 64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.141 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0683 time to fit residues: 0.8473 Evaluate side-chains 9 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.0070 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.044387 restraints weight = 59252.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045456 restraints weight = 39226.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046243 restraints weight = 28442.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.046804 restraints weight = 22099.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047205 restraints weight = 18276.068| |-----------------------------------------------------------------------------| r_work (final): 0.2966 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.038203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027873 restraints weight = 15249.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027866 restraints weight = 15856.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027678 restraints weight = 15913.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.027665 restraints weight = 15324.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.027653 restraints weight = 15554.117| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24964 Z= 0.132 Angle : 0.599 7.676 34164 Z= 0.325 Chirality : 0.042 0.175 4008 Planarity : 0.004 0.050 4416 Dihedral : 5.071 61.325 3584 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3340 helix: 0.74 (0.12), residues: 1960 sheet: 0.96 (0.38), residues: 172 loop : -0.13 (0.19), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 126 TYR 0.020 0.001 TYR A 428 PHE 0.023 0.002 PHE B 452 TRP 0.014 0.002 TRP D 250 HIS 0.005 0.001 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (24964) covalent geometry : angle 0.59923 / 0.32 (34164) hydrogen bonds : bond 0.04337 / 3.03 ( 1572) hydrogen bonds : angle 4.74716 / 3.45 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9606 (t80) cc_final: 0.9348 (t80) REVERT: B 365 TRP cc_start: 0.9423 (m100) cc_final: 0.9117 (m100) REVERT: B 366 MET cc_start: 0.9084 (mmp) cc_final: 0.8483 (ptp) REVERT: B 377 GLU cc_start: 0.9524 (tp30) cc_final: 0.9153 (tp30) REVERT: B 405 PHE cc_start: 0.9226 (p90) cc_final: 0.8949 (t80) REVERT: B 536 MET cc_start: 0.9403 (mmp) cc_final: 0.9132 (mmm) REVERT: B 568 MET cc_start: 0.9473 (mmp) cc_final: 0.9161 (mmp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0641 time to fit residues: 7.4128 Evaluate side-chains 66 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.179 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.031 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0196 time to fit residues: 0.3029 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 64 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 264 optimal weight: 0.0670 chunk 303 optimal weight: 0.0060 chunk 204 optimal weight: 0.1980 chunk 276 optimal weight: 0.0670 chunk 56 optimal weight: 10.0000 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.044510 restraints weight = 59425.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045560 restraints weight = 38747.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046311 restraints weight = 28087.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046824 restraints weight = 22047.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047215 restraints weight = 18415.930| |-----------------------------------------------------------------------------| r_work (final): 0.2992 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.037430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027253 restraints weight = 15377.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027253 restraints weight = 15016.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027253 restraints weight = 15016.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027253 restraints weight = 15016.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.027253 restraints weight = 15016.259| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24964 Z= 0.137 Angle : 0.600 7.311 34164 Z= 0.323 Chirality : 0.042 0.170 4008 Planarity : 0.004 0.072 4416 Dihedral : 4.921 59.974 3584 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.18 % Allowed : 2.52 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3340 helix: 0.94 (0.12), residues: 1948 sheet: 0.81 (0.38), residues: 152 loop : -0.07 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 537 TYR 0.018 0.001 TYR B 428 PHE 0.047 0.002 PHE A 468 TRP 0.021 0.001 TRP D 365 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (24964) covalent geometry : angle 0.60004 / 0.32 (34164) hydrogen bonds : bond 0.04064 / 2.86 ( 1572) hydrogen bonds : angle 4.58869 / 3.35 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9592 (t80) cc_final: 0.9351 (t80) REVERT: B 365 TRP cc_start: 0.9384 (m100) cc_final: 0.9040 (m100) REVERT: B 366 MET cc_start: 0.9115 (mmp) cc_final: 0.8536 (ptp) REVERT: B 377 GLU cc_start: 0.9504 (tp30) cc_final: 0.9154 (tp30) REVERT: B 378 ILE cc_start: 0.9099 (pt) cc_final: 0.8870 (pt) REVERT: B 405 PHE cc_start: 0.9129 (p90) cc_final: 0.8900 (t80) REVERT: B 449 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9093 (mt-10) REVERT: B 536 MET cc_start: 0.9403 (mmp) cc_final: 0.9062 (mmm) REVERT: B 539 ASP cc_start: 0.9294 (t70) cc_final: 0.9009 (m-30) REVERT: B 568 MET cc_start: 0.9453 (mmp) cc_final: 0.9167 (mmp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0575 time to fit residues: 6.3793 Evaluate side-chains 67 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.199 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0204 time to fit residues: 0.3131 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 190 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 254 optimal weight: 4.9990 chunk 314 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 0.0020 chunk 234 optimal weight: 5.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.056017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044577 restraints weight = 58795.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045626 restraints weight = 38226.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046396 restraints weight = 27802.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046936 restraints weight = 21586.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047310 restraints weight = 17975.670| |-----------------------------------------------------------------------------| r_work (final): 0.2990 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.037278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027271 restraints weight = 15857.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027280 restraints weight = 15336.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.027398 restraints weight = 14523.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.027515 restraints weight = 12889.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.027437 restraints weight = 13653.174| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24964 Z= 0.113 Angle : 0.548 6.676 34164 Z= 0.294 Chirality : 0.041 0.164 4008 Planarity : 0.003 0.041 4416 Dihedral : 4.619 56.460 3584 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3340 helix: 1.07 (0.12), residues: 1952 sheet: 0.99 (0.35), residues: 204 loop : -0.15 (0.20), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 126 TYR 0.017 0.001 TYR B 428 PHE 0.021 0.001 PHE B 229 TRP 0.016 0.001 TRP B 391 HIS 0.004 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (24964) covalent geometry : angle 0.54760 / 0.29 (34164) hydrogen bonds : bond 0.03519 / 2.46 ( 1572) hydrogen bonds : angle 4.35488 / 3.18 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9565 (t80) cc_final: 0.9267 (t80) REVERT: B 365 TRP cc_start: 0.9335 (m100) cc_final: 0.9036 (m100) REVERT: B 366 MET cc_start: 0.9226 (mmp) cc_final: 0.8803 (ptp) REVERT: B 377 GLU cc_start: 0.9529 (tp30) cc_final: 0.9115 (tp30) REVERT: B 405 PHE cc_start: 0.9125 (p90) cc_final: 0.8918 (t80) REVERT: B 449 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9070 (mt-10) REVERT: B 468 PHE cc_start: 0.9459 (m-10) cc_final: 0.9152 (t80) REVERT: B 536 MET cc_start: 0.9426 (mmp) cc_final: 0.8996 (mmt) REVERT: B 539 ASP cc_start: 0.9337 (t70) cc_final: 0.8978 (m-30) REVERT: B 568 MET cc_start: 0.9451 (mmp) cc_final: 0.9170 (mmp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0600 time to fit residues: 6.4851 Evaluate side-chains 62 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.164 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0191 time to fit residues: 0.2996 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 95 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 317 optimal weight: 0.0030 chunk 76 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 0.0000 chunk 164 optimal weight: 6.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.043732 restraints weight = 60419.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044761 restraints weight = 39577.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.045541 restraints weight = 28777.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046073 restraints weight = 22287.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.046454 restraints weight = 18493.977| |-----------------------------------------------------------------------------| r_work (final): 0.2971 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.037046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.027151 restraints weight = 16090.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027292 restraints weight = 15060.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.027484 restraints weight = 12664.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.027475 restraints weight = 13345.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.027468 restraints weight = 13376.709| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24964 Z= 0.109 Angle : 0.538 6.554 34164 Z= 0.288 Chirality : 0.040 0.199 4008 Planarity : 0.003 0.046 4416 Dihedral : 4.440 51.263 3584 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3340 helix: 1.18 (0.12), residues: 1940 sheet: 1.54 (0.37), residues: 188 loop : -0.11 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 126 TYR 0.018 0.001 TYR B 499 PHE 0.013 0.001 PHE D 241 TRP 0.013 0.001 TRP C 365 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (24964) covalent geometry : angle 0.53778 / 0.29 (34164) hydrogen bonds : bond 0.03353 / 2.34 ( 1572) hydrogen bonds : angle 4.29481 / 3.13 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9751 (tp) cc_final: 0.9536 (mt) REVERT: B 359 PHE cc_start: 0.9584 (t80) cc_final: 0.9154 (t80) REVERT: B 365 TRP cc_start: 0.9272 (m100) cc_final: 0.8954 (m100) REVERT: B 366 MET cc_start: 0.9273 (mmp) cc_final: 0.8737 (ptp) REVERT: B 377 GLU cc_start: 0.9553 (tp30) cc_final: 0.9176 (tp30) REVERT: B 405 PHE cc_start: 0.9177 (p90) cc_final: 0.8902 (t80) REVERT: B 536 MET cc_start: 0.9455 (mmp) cc_final: 0.9063 (mmt) REVERT: B 539 ASP cc_start: 0.9431 (t70) cc_final: 0.9034 (m-30) REVERT: B 568 MET cc_start: 0.9434 (mmp) cc_final: 0.9201 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0552 time to fit residues: 5.9562 Evaluate side-chains 64 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.198 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.038 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0198 time to fit residues: 0.3084 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 204 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 308 optimal weight: 30.0000 chunk 69 optimal weight: 40.0000 chunk 175 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 280 optimal weight: 40.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.042128 restraints weight = 61589.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043115 restraints weight = 40327.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043821 restraints weight = 29315.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044313 restraints weight = 23046.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044669 restraints weight = 19293.296| |-----------------------------------------------------------------------------| r_work (final): 0.2921 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.036880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.026639 restraints weight = 16029.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026716 restraints weight = 15383.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026716 restraints weight = 14327.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026716 restraints weight = 14334.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.026716 restraints weight = 14334.128| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24964 Z= 0.169 Angle : 0.575 6.426 34164 Z= 0.311 Chirality : 0.041 0.179 4008 Planarity : 0.004 0.048 4416 Dihedral : 4.503 43.696 3584 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3340 helix: 1.23 (0.12), residues: 1948 sheet: 1.43 (0.38), residues: 204 loop : -0.05 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 493 TYR 0.018 0.002 TYR A 44 PHE 0.021 0.002 PHE C 468 TRP 0.023 0.002 TRP B 391 HIS 0.004 0.001 HIS D 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (24964) covalent geometry : angle 0.57486 / 0.31 (34164) hydrogen bonds : bond 0.03428 / 2.38 ( 1572) hydrogen bonds : angle 4.35351 / 3.18 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9587 (t80) cc_final: 0.9139 (t80) REVERT: B 359 PHE cc_start: 0.9617 (t80) cc_final: 0.9357 (t80) REVERT: B 365 TRP cc_start: 0.9252 (m100) cc_final: 0.8972 (m100) REVERT: B 366 MET cc_start: 0.9343 (mmp) cc_final: 0.8780 (ptp) REVERT: B 377 GLU cc_start: 0.9625 (tp30) cc_final: 0.9296 (tp30) REVERT: B 378 ILE cc_start: 0.9206 (pt) cc_final: 0.8924 (pt) REVERT: B 468 PHE cc_start: 0.9450 (m-80) cc_final: 0.9106 (m-80) REVERT: B 536 MET cc_start: 0.9543 (mmp) cc_final: 0.9212 (mmt) REVERT: B 539 ASP cc_start: 0.9506 (t70) cc_final: 0.9099 (m-30) REVERT: B 568 MET cc_start: 0.9415 (mmp) cc_final: 0.9125 (mmp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0494 time to fit residues: 5.1013 Evaluate side-chains 56 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.171 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0219 time to fit residues: 0.3232 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 315 optimal weight: 50.0000 chunk 177 optimal weight: 20.0000 chunk 322 optimal weight: 50.0000 chunk 280 optimal weight: 50.0000 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 303 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 GLN B 470 ASN B 662 HIS ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040406 restraints weight = 63071.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.041334 restraints weight = 41304.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041998 restraints weight = 30158.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.042457 restraints weight = 23735.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.042795 restraints weight = 19964.922| |-----------------------------------------------------------------------------| r_work (final): 0.2869 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.036469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.026748 restraints weight = 15961.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.026707 restraints weight = 14003.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.026695 restraints weight = 14969.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.026695 restraints weight = 15169.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.026695 restraints weight = 15169.193| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24964 Z= 0.244 Angle : 0.656 6.372 34164 Z= 0.364 Chirality : 0.042 0.169 4008 Planarity : 0.005 0.047 4416 Dihedral : 4.830 29.410 3584 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 3340 helix: 0.97 (0.12), residues: 1948 sheet: 0.94 (0.38), residues: 204 loop : -0.19 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 104 TYR 0.028 0.002 TYR B 428 PHE 0.017 0.002 PHE B 269 TRP 0.019 0.002 TRP B 413 HIS 0.005 0.002 HIS D 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.24 (24964) covalent geometry : angle 0.65625 / 0.36 (34164) hydrogen bonds : bond 0.04006 / 2.76 ( 1572) hydrogen bonds : angle 4.74231 / 3.47 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.159 Fit side-chains REVERT: B 49 PHE cc_start: 0.9626 (t80) cc_final: 0.9170 (t80) REVERT: B 359 PHE cc_start: 0.9584 (t80) cc_final: 0.9264 (t80) REVERT: B 365 TRP cc_start: 0.9199 (m100) cc_final: 0.8934 (m100) REVERT: B 366 MET cc_start: 0.9312 (mmp) cc_final: 0.8731 (ptp) REVERT: B 377 GLU cc_start: 0.9579 (tp30) cc_final: 0.9265 (tp30) REVERT: B 424 ILE cc_start: 0.9369 (pt) cc_final: 0.8788 (pt) REVERT: B 568 MET cc_start: 0.9424 (mmp) cc_final: 0.9163 (mmp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0428 time to fit residues: 4.6923 Evaluate side-chains 55 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.197 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: F 119 GLU cc_start: 0.9557 (tp30) cc_final: 0.9352 (tp30) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0193 time to fit residues: 0.3031 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 127 optimal weight: 10.0000 chunk 30 optimal weight: 50.0000 chunk 11 optimal weight: 0.6980 chunk 270 optimal weight: 0.0470 chunk 335 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 164 optimal weight: 0.0570 chunk 172 optimal weight: 5.9990 chunk 312 optimal weight: 30.0000 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042208 restraints weight = 61262.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043214 restraints weight = 39402.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043917 restraints weight = 28276.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044434 restraints weight = 22031.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044810 restraints weight = 18342.829| |-----------------------------------------------------------------------------| r_work (final): 0.2925 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.037316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027246 restraints weight = 16304.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.027225 restraints weight = 16700.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.027217 restraints weight = 14883.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.027212 restraints weight = 15153.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.027207 restraints weight = 15284.756| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24964 Z= 0.116 Angle : 0.586 7.425 34164 Z= 0.312 Chirality : 0.042 0.235 4008 Planarity : 0.003 0.028 4416 Dihedral : 4.422 26.151 3584 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3340 helix: 1.10 (0.12), residues: 1952 sheet: 0.86 (0.40), residues: 176 loop : -0.01 (0.20), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 126 TYR 0.024 0.002 TYR D 428 PHE 0.020 0.002 PHE A 241 TRP 0.030 0.002 TRP D 365 HIS 0.009 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (24964) covalent geometry : angle 0.58586 / 0.31 (34164) hydrogen bonds : bond 0.03417 / 2.37 ( 1572) hydrogen bonds : angle 4.43238 / 3.26 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9634 (t80) cc_final: 0.9156 (t80) REVERT: B 359 PHE cc_start: 0.9553 (t80) cc_final: 0.9237 (t80) REVERT: B 365 TRP cc_start: 0.9359 (m100) cc_final: 0.9074 (m100) REVERT: B 366 MET cc_start: 0.9215 (mmp) cc_final: 0.8616 (ptp) REVERT: B 377 GLU cc_start: 0.9535 (tp30) cc_final: 0.9134 (tp30) REVERT: B 378 ILE cc_start: 0.9214 (pt) cc_final: 0.8905 (pt) REVERT: B 424 ILE cc_start: 0.9399 (pt) cc_final: 0.8821 (pt) REVERT: B 429 PHE cc_start: 0.9221 (t80) cc_final: 0.8702 (t80) REVERT: B 568 MET cc_start: 0.9471 (mmp) cc_final: 0.9240 (mmp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0517 time to fit residues: 5.4962 Evaluate side-chains 57 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.163 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0171 time to fit residues: 0.2719 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 299 optimal weight: 0.0040 chunk 73 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 227 optimal weight: 50.0000 chunk 276 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 203 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 80 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.7514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042477 restraints weight = 60682.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.043463 restraints weight = 39343.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044183 restraints weight = 28506.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044700 restraints weight = 22254.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045045 restraints weight = 18558.665| |-----------------------------------------------------------------------------| r_work (final): 0.2929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.036991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.027177 restraints weight = 16050.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.027052 restraints weight = 17102.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027050 restraints weight = 15851.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027050 restraints weight = 15921.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027050 restraints weight = 15921.599| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24964 Z= 0.114 Angle : 0.587 8.290 34164 Z= 0.311 Chirality : 0.042 0.226 4008 Planarity : 0.003 0.028 4416 Dihedral : 4.178 22.152 3584 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3340 helix: 1.20 (0.12), residues: 1952 sheet: 0.80 (0.37), residues: 204 loop : 0.03 (0.20), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 675 TYR 0.023 0.002 TYR D 428 PHE 0.019 0.001 PHE A 475 TRP 0.029 0.002 TRP A 370 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (24964) covalent geometry : angle 0.58743 / 0.31 (34164) hydrogen bonds : bond 0.03323 / 2.31 ( 1572) hydrogen bonds : angle 4.36438 / 3.20 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9635 (t80) cc_final: 0.9143 (t80) REVERT: B 258 ASP cc_start: 0.6468 (m-30) cc_final: 0.6128 (t0) REVERT: B 359 PHE cc_start: 0.9521 (t80) cc_final: 0.9195 (t80) REVERT: B 365 TRP cc_start: 0.9323 (m100) cc_final: 0.9080 (m100) REVERT: B 366 MET cc_start: 0.9246 (mmp) cc_final: 0.8635 (ptp) REVERT: B 370 TRP cc_start: 0.8851 (t-100) cc_final: 0.8322 (t-100) REVERT: B 377 GLU cc_start: 0.9510 (tp30) cc_final: 0.9119 (tp30) REVERT: B 378 ILE cc_start: 0.9127 (pt) cc_final: 0.8910 (pt) REVERT: B 424 ILE cc_start: 0.9414 (pt) cc_final: 0.8794 (pt) REVERT: B 429 PHE cc_start: 0.9142 (t80) cc_final: 0.8712 (t80) REVERT: B 435 THR cc_start: 0.9369 (p) cc_final: 0.9017 (p) REVERT: B 568 MET cc_start: 0.9469 (mmp) cc_final: 0.9242 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0508 time to fit residues: 5.3347 Evaluate side-chains 58 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.202 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0192 time to fit residues: 0.3012 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 279 optimal weight: 30.0000 chunk 327 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 302 optimal weight: 40.0000 chunk 21 optimal weight: 0.0170 chunk 171 optimal weight: 0.6980 chunk 328 optimal weight: 7.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.043067 restraints weight = 60259.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044064 restraints weight = 39080.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044807 restraints weight = 28490.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045337 restraints weight = 22225.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045715 restraints weight = 18506.199| |-----------------------------------------------------------------------------| r_work (final): 0.2925 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.037023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027135 restraints weight = 16124.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027128 restraints weight = 15215.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.027120 restraints weight = 15307.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.027120 restraints weight = 15392.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.027120 restraints weight = 15392.705| |-----------------------------------------------------------------------------| r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24964 Z= 0.113 Angle : 0.590 7.198 34164 Z= 0.311 Chirality : 0.042 0.210 4008 Planarity : 0.003 0.028 4416 Dihedral : 3.991 21.792 3584 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3340 helix: 1.26 (0.12), residues: 1952 sheet: 1.11 (0.38), residues: 204 loop : -0.03 (0.20), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 493 TYR 0.021 0.001 TYR D 464 PHE 0.025 0.001 PHE C 229 TRP 0.031 0.002 TRP D 370 HIS 0.007 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (24964) covalent geometry : angle 0.59025 / 0.31 (34164) hydrogen bonds : bond 0.03334 / 2.33 ( 1572) hydrogen bonds : angle 4.29385 / 3.14 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 PHE cc_start: 0.9657 (t80) cc_final: 0.9217 (t80) REVERT: B 258 ASP cc_start: 0.6566 (m-30) cc_final: 0.6200 (t0) REVERT: B 359 PHE cc_start: 0.9478 (t80) cc_final: 0.9139 (t80) REVERT: B 365 TRP cc_start: 0.9347 (m100) cc_final: 0.9094 (m100) REVERT: B 366 MET cc_start: 0.9279 (mmp) cc_final: 0.8698 (ptp) REVERT: B 370 TRP cc_start: 0.8748 (t-100) cc_final: 0.8282 (t-100) REVERT: B 377 GLU cc_start: 0.9549 (tp30) cc_final: 0.9331 (tp30) REVERT: B 378 ILE cc_start: 0.9036 (pt) cc_final: 0.8825 (pt) REVERT: B 424 ILE cc_start: 0.9485 (pt) cc_final: 0.8892 (pt) REVERT: B 429 PHE cc_start: 0.9056 (t80) cc_final: 0.8662 (t80) REVERT: B 435 THR cc_start: 0.9377 (p) cc_final: 0.9000 (p) REVERT: B 568 MET cc_start: 0.9496 (mmp) cc_final: 0.9267 (mmp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0504 time to fit residues: 5.3957 Evaluate side-chains 59 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.197 Evaluate side-chains 11 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0139 time to fit residues: 0.2197 Evaluate side-chains 10 residues out of total 121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 290 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 131 optimal weight: 0.0170 chunk 209 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 328 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 470 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.042342 restraints weight = 61648.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043341 restraints weight = 40023.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044069 restraints weight = 29031.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.044594 restraints weight = 22554.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.044965 restraints weight = 18752.180| |-----------------------------------------------------------------------------| r_work (final): 0.2904 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.037184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.027295 restraints weight = 15641.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.027180 restraints weight = 16584.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027177 restraints weight = 15263.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027172 restraints weight = 15350.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027172 restraints weight = 15458.866| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24964 Z= 0.114 Angle : 0.566 6.717 34164 Z= 0.302 Chirality : 0.041 0.205 4008 Planarity : 0.003 0.039 4416 Dihedral : 3.952 22.068 3584 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3340 helix: 1.29 (0.12), residues: 1968 sheet: 1.10 (0.37), residues: 208 loop : 0.06 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 493 TYR 0.025 0.001 TYR B 464 PHE 0.014 0.001 PHE B 241 TRP 0.030 0.002 TRP D 370 HIS 0.007 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24964) covalent geometry : angle 0.56585 / 0.30 (34164) hydrogen bonds : bond 0.03248 / 2.26 ( 1572) hydrogen bonds : angle 4.28249 / 3.14 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.02 seconds wall clock time: 37 minutes 3.84 seconds (2223.84 seconds total)