Starting phenix.real_space_refine on Fri Jul 3 22:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpw_74535/07_2026/9zpw_74535.map" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 6 8.98 5 P 28 5.49 5 S 76 5.16 5 C 10601 2.51 5 N 2400 2.21 5 O 2896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16007 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "B" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "C" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "D" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3680 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain: "A" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 323 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 5 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 357 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 283 Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'PCW:plan-4': 2, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 318 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'CLR': 1, 'PCG': 1, 'PCW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'PCW:plan-2': 4, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 3.78, per 1000 atoms: 0.24 Number of scatterers: 16007 At special positions: 0 Unit cell: (98.1, 98.1, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 6 19.00 S 76 16.00 P 28 15.00 O 2896 8.00 N 2400 7.00 C 10601 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: 1.40 Conformation dependent library (CDL) restraints added in 598.0 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 68.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.543A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.063A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.742A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.924A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.871A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.628A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.002A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 458 through 477 removed outlier: 5.544A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.094A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 588 removed outlier: 4.124A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.543A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.092A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.505A pdb=" N GLN B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.918A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.869A pdb=" N LEU B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.628A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.996A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 404 through 425 Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 458 through 477 removed outlier: 5.549A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 485 through 493 removed outlier: 3.988A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 588 removed outlier: 4.110A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.542A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.062A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.507A pdb=" N GLN C 193 " --> pdb=" O PHE C 189 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.924A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.874A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.629A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.998A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 404 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 458 through 477 removed outlier: 5.538A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 485 through 493 removed outlier: 3.993A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 4.084A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 603 removed outlier: 3.840A pdb=" N LEU C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.544A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.054A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.738A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.920A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.873A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.636A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.997A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 404 Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 458 through 477 removed outlier: 5.573A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 485 through 493 removed outlier: 4.224A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 removed outlier: 3.895A pdb=" N LEU D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 588 removed outlier: 4.034A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR D 588 " --> pdb=" O ALA D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 592 through 603 removed outlier: 3.579A pdb=" N GLY D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.566A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.543A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS A 507 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 6.540A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR B 517 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.536A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 507 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B 536 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.537A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.534A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C 507 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.558A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.538A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2428 1.31 - 1.44: 4357 1.44 - 1.57: 9352 1.57 - 1.69: 60 1.69 - 1.82: 140 Bond restraints: 16337 Sorted by residual: bond pdb=" C2' PCG D 703 " pdb=" C3' PCG D 703 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C2' PCG C 702 " pdb=" C3' PCG C 702 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C2' PCG A 701 " pdb=" C3' PCG A 701 " ideal model delta sigma weight residual 1.514 1.195 0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C2' PCG B 702 " pdb=" C3' PCG B 702 " ideal model delta sigma weight residual 1.514 1.196 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" C3' PCG D 703 " pdb=" C4' PCG D 703 " ideal model delta sigma weight residual 1.519 1.814 -0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 16332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 21661 2.07 - 4.14: 180 4.14 - 6.20: 53 6.20 - 8.27: 45 8.27 - 10.34: 26 Bond angle restraints: 21965 Sorted by residual: angle pdb=" CA GLN C 601 " pdb=" CB GLN C 601 " pdb=" CG GLN C 601 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA GLN A 601 " pdb=" CB GLN A 601 " pdb=" CG GLN A 601 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLN D 601 " pdb=" CB GLN D 601 " pdb=" CG GLN D 601 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CA GLN B 601 " pdb=" CB GLN B 601 " pdb=" CG GLN B 601 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" C5' PCG D 703 " pdb=" O5' PCG D 703 " pdb=" PA PCG D 703 " ideal model delta sigma weight residual 121.82 111.48 10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 21960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.17: 9666 31.17 - 62.34: 518 62.34 - 93.51: 42 93.51 - 124.68: 0 124.68 - 155.84: 4 Dihedral angle restraints: 10230 sinusoidal: 4918 harmonic: 5312 Sorted by residual: dihedral pdb=" CA ASP D 482 " pdb=" C ASP D 482 " pdb=" N CYS D 483 " pdb=" CA CYS D 483 " ideal model delta harmonic sigma weight residual -180.00 -154.95 -25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP B 482 " pdb=" C ASP B 482 " pdb=" N CYS B 483 " pdb=" CA CYS B 483 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP C 482 " pdb=" C ASP C 482 " pdb=" N CYS C 483 " pdb=" CA CYS C 483 " ideal model delta harmonic sigma weight residual -180.00 -156.08 -23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 10227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2308 0.102 - 0.203: 52 0.203 - 0.305: 0 0.305 - 0.406: 8 0.406 - 0.508: 4 Chirality restraints: 2372 Sorted by residual: chirality pdb=" PA PCG D 703 " pdb=" O2A PCG D 703 " pdb=" O3' PCG D 703 " pdb=" O5' PCG D 703 " both_signs ideal model delta sigma weight residual True 2.70 3.21 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" PA PCG B 702 " pdb=" O2A PCG B 702 " pdb=" O3' PCG B 702 " pdb=" O5' PCG B 702 " both_signs ideal model delta sigma weight residual True 2.70 3.21 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" PA PCG C 702 " pdb=" O2A PCG C 702 " pdb=" O3' PCG C 702 " pdb=" O5' PCG C 702 " both_signs ideal model delta sigma weight residual True 2.70 3.20 -0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 2369 not shown) Planarity restraints: 2627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 485 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ALA B 485 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA B 485 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY B 486 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 485 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ALA C 485 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA C 485 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 486 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 485 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C ALA D 485 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA D 485 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY D 486 " 0.012 2.00e-02 2.50e+03 ... (remaining 2624 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 5277 2.84 - 3.42: 17454 3.42 - 3.99: 30737 3.99 - 4.57: 44889 4.57 - 5.14: 63062 Nonbonded interactions: 161419 Sorted by model distance: nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.265 3.040 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.268 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.269 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.288 3.040 ... (remaining 161414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C4 or name C5 or name O11 or name O1P \ or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P \ )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37)) or (resid 707 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C39 or name C40 or name O2 or name O3 or name O31 or nam \ e O3P)) or (resid 708 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name O3 or name O31 \ or name O3P)))) selection = (chain 'B' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C4 or name C5 or name O11 or name O1P \ or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P \ )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C3 or name C31)) or (resid 707 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C39 or name C40 or name O2 or name O3 or name O31 or nam \ e O3P)) or (resid 708 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name O3 or name O31 \ or name O3P)))) selection = (chain 'C' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C4 or name C5 or name O11 or name O1P \ or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P \ )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37)) or (resid 707 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C39 or name C40 or name O2 or name O3 or name O31 or nam \ e O3P)) or (resid 708 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C2 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C4 or name C40 or name C41 or name O3 or name O31 o \ r name O3P)))) selection = (chain 'D' and (resid 156 through 604 or (resid 705 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C4 or name C5 or name O11 or name O1P \ or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P \ )) or (resid 706 and (name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 \ or name C36 or name C37)) or (resid 707 and (name C1 or name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C39 or name C40 or name O2 or name O3 or name O31 or nam \ e O3P)) or (resid 708 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name O3 or name O31 \ or name O3P)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.250 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: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 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 : 0.011 0.319 16337 Z= 0.534 Angle : 0.674 10.341 21965 Z= 0.295 Chirality : 0.048 0.508 2372 Planarity : 0.002 0.029 2627 Dihedral : 17.776 155.845 6822 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.93 % Allowed : 26.42 % Favored : 72.65 % 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: 2.32 (0.21), residues: 1788 helix: 2.28 (0.15), residues: 1216 sheet: 3.63 (0.55), residues: 48 loop : -0.49 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.011 0.001 TYR A 349 PHE 0.006 0.001 PHE D 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.000 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.53 (16337) covalent geometry : angle 0.67409 / 0.30 (21965) hydrogen bonds : bond 0.10589 / 6.72 ( 930) hydrogen bonds : angle 3.75052 / 2.68 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.606 Fit side-chains REVERT: A 305 MET cc_start: 0.9046 (ttm) cc_final: 0.8757 (ttp) REVERT: A 476 LYS cc_start: 0.8544 (mmpt) cc_final: 0.8295 (mttt) REVERT: B 234 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8655 (tm) REVERT: B 305 MET cc_start: 0.9065 (ttm) cc_final: 0.8775 (ttp) REVERT: B 476 LYS cc_start: 0.8602 (mmpt) cc_final: 0.8261 (mttt) REVERT: B 496 GLN cc_start: 0.8972 (mt0) cc_final: 0.8649 (mm-40) REVERT: C 305 MET cc_start: 0.9058 (ttm) cc_final: 0.8774 (ttp) REVERT: C 476 LYS cc_start: 0.8602 (mmpt) cc_final: 0.8274 (mttt) REVERT: C 496 GLN cc_start: 0.8955 (mt0) cc_final: 0.8603 (mm-40) REVERT: D 305 MET cc_start: 0.9062 (ttm) cc_final: 0.8761 (ttp) REVERT: D 476 LYS cc_start: 0.8595 (mmpt) cc_final: 0.8257 (mttt) REVERT: D 487 LEU cc_start: 0.8743 (mt) cc_final: 0.8387 (pt) REVERT: D 496 GLN cc_start: 0.8953 (mt0) cc_final: 0.8607 (mm-40) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.7417 time to fit residues: 98.2552 Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 603 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.097076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065198 restraints weight = 28790.499| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.06 r_work: 0.2785 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16337 Z= 0.105 Angle : 0.466 6.724 21965 Z= 0.241 Chirality : 0.038 0.144 2372 Planarity : 0.003 0.029 2627 Dihedral : 14.069 156.776 3276 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.90 % Allowed : 22.90 % Favored : 74.20 % 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: 2.58 (0.21), residues: 1788 helix: 2.54 (0.15), residues: 1184 sheet: 2.77 (0.54), residues: 48 loop : -0.26 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.012 0.001 TYR B 349 PHE 0.009 0.001 PHE A 298 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16337) covalent geometry : angle 0.46565 / 0.24 (21965) hydrogen bonds : bond 0.03604 / 2.38 ( 930) hydrogen bonds : angle 3.45632 / 2.47 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.638 Fit side-chains REVERT: A 305 MET cc_start: 0.9059 (ttm) cc_final: 0.8777 (ttp) REVERT: A 411 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8748 (tp40) REVERT: A 476 LYS cc_start: 0.8692 (mmpt) cc_final: 0.8410 (mttt) REVERT: B 234 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8667 (tm) REVERT: B 305 MET cc_start: 0.9067 (ttm) cc_final: 0.8792 (ttp) REVERT: B 411 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8749 (tp40) REVERT: B 476 LYS cc_start: 0.8695 (mmpt) cc_final: 0.8307 (mttt) REVERT: B 496 GLN cc_start: 0.9262 (mt0) cc_final: 0.8867 (mm-40) REVERT: C 305 MET cc_start: 0.9049 (ttm) cc_final: 0.8777 (ttp) REVERT: C 476 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8374 (mttt) REVERT: C 496 GLN cc_start: 0.9235 (mt0) cc_final: 0.8832 (mm-40) REVERT: D 305 MET cc_start: 0.9071 (ttm) cc_final: 0.8791 (ttp) REVERT: D 476 LYS cc_start: 0.8724 (mmpt) cc_final: 0.8357 (mttt) REVERT: D 487 LEU cc_start: 0.8753 (mt) cc_final: 0.8395 (pt) REVERT: D 496 GLN cc_start: 0.9231 (mt0) cc_final: 0.8846 (mm-40) REVERT: D 604 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6256 (ppp) outliers start: 47 outliers final: 7 residues processed: 156 average time/residue: 0.6408 time to fit residues: 110.6684 Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 604 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 175 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.063894 restraints weight = 29158.585| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.09 r_work: 0.2756 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16337 Z= 0.134 Angle : 0.479 7.451 21965 Z= 0.247 Chirality : 0.039 0.156 2372 Planarity : 0.003 0.029 2627 Dihedral : 14.192 157.066 3264 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.40 % Allowed : 23.27 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.21), residues: 1788 helix: 2.55 (0.15), residues: 1184 sheet: 2.23 (0.54), residues: 48 loop : -0.30 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.012 0.001 TYR B 349 PHE 0.011 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16337) covalent geometry : angle 0.47906 / 0.25 (21965) hydrogen bonds : bond 0.03771 / 2.50 ( 930) hydrogen bonds : angle 3.45958 / 2.47 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 0.635 Fit side-chains REVERT: A 305 MET cc_start: 0.9067 (ttm) cc_final: 0.8789 (ttp) REVERT: A 411 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8651 (tp40) REVERT: A 476 LYS cc_start: 0.8701 (mmpt) cc_final: 0.8379 (mttt) REVERT: B 234 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8664 (tm) REVERT: B 305 MET cc_start: 0.9069 (ttm) cc_final: 0.8780 (ttp) REVERT: B 411 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8659 (tp40) REVERT: B 476 LYS cc_start: 0.8687 (mmpt) cc_final: 0.8310 (mttt) REVERT: B 496 GLN cc_start: 0.9260 (mt0) cc_final: 0.8900 (mm-40) REVERT: C 305 MET cc_start: 0.9057 (ttm) cc_final: 0.8770 (ttp) REVERT: C 476 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8371 (mttt) REVERT: C 496 GLN cc_start: 0.9243 (mt0) cc_final: 0.8882 (mm-40) REVERT: D 476 LYS cc_start: 0.8699 (mmpt) cc_final: 0.8344 (mttt) REVERT: D 487 LEU cc_start: 0.8747 (mt) cc_final: 0.8399 (pt) REVERT: D 496 GLN cc_start: 0.9234 (mt0) cc_final: 0.8840 (mm-40) outliers start: 55 outliers final: 10 residues processed: 158 average time/residue: 0.5417 time to fit residues: 95.8002 Evaluate side-chains 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 429 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.062692 restraints weight = 28897.590| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.07 r_work: 0.2729 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16337 Z= 0.186 Angle : 0.515 7.951 21965 Z= 0.265 Chirality : 0.040 0.187 2372 Planarity : 0.003 0.029 2627 Dihedral : 14.621 156.800 3264 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.83 % Allowed : 22.59 % Favored : 73.58 % 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: 2.43 (0.21), residues: 1788 helix: 2.47 (0.15), residues: 1184 sheet: 2.04 (0.54), residues: 48 loop : -0.36 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.014 0.001 TYR C 349 PHE 0.013 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (16337) covalent geometry : angle 0.51494 / 0.26 (21965) hydrogen bonds : bond 0.04146 / 2.75 ( 930) hydrogen bonds : angle 3.56897 / 2.56 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 110 time to evaluate : 0.635 Fit side-chains REVERT: A 411 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8605 (tp40) REVERT: A 476 LYS cc_start: 0.8735 (mmpt) cc_final: 0.8400 (mttt) REVERT: B 234 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8673 (tm) REVERT: B 411 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8615 (tp40) REVERT: B 476 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8287 (mttt) REVERT: B 496 GLN cc_start: 0.9257 (mt0) cc_final: 0.8896 (mm-40) REVERT: C 476 LYS cc_start: 0.8756 (mmpt) cc_final: 0.8385 (mttt) REVERT: C 496 GLN cc_start: 0.9240 (mt0) cc_final: 0.8924 (mm-40) REVERT: D 476 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8300 (mttt) REVERT: D 487 LEU cc_start: 0.8750 (mt) cc_final: 0.8409 (pt) REVERT: D 496 GLN cc_start: 0.9239 (mt0) cc_final: 0.8903 (mm-40) outliers start: 62 outliers final: 19 residues processed: 164 average time/residue: 0.5587 time to fit residues: 102.2817 Evaluate side-chains 130 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 95 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 150 optimal weight: 0.0060 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063461 restraints weight = 28891.733| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.07 r_work: 0.2746 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16337 Z= 0.143 Angle : 0.497 8.437 21965 Z= 0.255 Chirality : 0.039 0.164 2372 Planarity : 0.003 0.029 2627 Dihedral : 14.475 157.274 3264 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.27 % Allowed : 23.33 % Favored : 73.40 % 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: 2.44 (0.21), residues: 1788 helix: 2.50 (0.15), residues: 1184 sheet: 1.88 (0.55), residues: 48 loop : -0.38 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 287 TYR 0.013 0.001 TYR A 349 PHE 0.011 0.001 PHE A 298 TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16337) covalent geometry : angle 0.49679 / 0.26 (21965) hydrogen bonds : bond 0.03872 / 2.57 ( 930) hydrogen bonds : angle 3.50870 / 2.52 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.572 Fit side-chains REVERT: A 411 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8603 (tp40) REVERT: A 476 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8390 (mttt) REVERT: B 234 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8669 (tm) REVERT: B 411 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8605 (tp40) REVERT: B 476 LYS cc_start: 0.8702 (mmpt) cc_final: 0.8299 (mttt) REVERT: B 496 GLN cc_start: 0.9271 (mt0) cc_final: 0.8914 (mm-40) REVERT: C 476 LYS cc_start: 0.8764 (mmpt) cc_final: 0.8403 (mttt) REVERT: C 496 GLN cc_start: 0.9254 (mt0) cc_final: 0.8897 (mm-40) REVERT: D 476 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8339 (mttt) REVERT: D 487 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8381 (pt) REVERT: D 496 GLN cc_start: 0.9244 (mt0) cc_final: 0.8857 (mm-40) outliers start: 53 outliers final: 13 residues processed: 153 average time/residue: 0.5818 time to fit residues: 99.2351 Evaluate side-chains 125 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 0.0980 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 83 optimal weight: 0.0370 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065463 restraints weight = 28949.965| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.07 r_work: 0.2792 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16337 Z= 0.096 Angle : 0.473 8.162 21965 Z= 0.241 Chirality : 0.038 0.144 2372 Planarity : 0.002 0.028 2627 Dihedral : 13.898 158.563 3264 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.98 % Allowed : 24.88 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.21), residues: 1788 helix: 2.57 (0.15), residues: 1184 sheet: 1.81 (0.55), residues: 48 loop : -0.35 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 287 TYR 0.011 0.001 TYR B 349 PHE 0.007 0.001 PHE B 410 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (16337) covalent geometry : angle 0.47290 / 0.24 (21965) hydrogen bonds : bond 0.03323 / 2.21 ( 930) hydrogen bonds : angle 3.37451 / 2.42 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.605 Fit side-chains REVERT: A 305 MET cc_start: 0.9053 (ttm) cc_final: 0.8767 (ttp) REVERT: A 411 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8638 (tp40) REVERT: A 476 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8437 (mttt) REVERT: A 590 ASP cc_start: 0.8535 (p0) cc_final: 0.8181 (p0) REVERT: B 234 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (tm) REVERT: B 305 MET cc_start: 0.9065 (ttm) cc_final: 0.8788 (ttp) REVERT: B 411 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (tp40) REVERT: B 476 LYS cc_start: 0.8759 (mmpt) cc_final: 0.8398 (mttt) REVERT: B 496 GLN cc_start: 0.9275 (mt0) cc_final: 0.8983 (mm-40) REVERT: C 305 MET cc_start: 0.9065 (ttm) cc_final: 0.8787 (ttp) REVERT: C 476 LYS cc_start: 0.8758 (mmpt) cc_final: 0.8397 (mttt) REVERT: C 496 GLN cc_start: 0.9254 (mt0) cc_final: 0.8961 (mm-40) REVERT: D 305 MET cc_start: 0.9062 (ttm) cc_final: 0.8775 (ttp) REVERT: D 476 LYS cc_start: 0.8731 (mmpt) cc_final: 0.8393 (mttt) REVERT: D 487 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8381 (pt) REVERT: D 496 GLN cc_start: 0.9257 (mt0) cc_final: 0.8961 (mm-40) REVERT: D 590 ASP cc_start: 0.8378 (p0) cc_final: 0.8160 (p0) outliers start: 32 outliers final: 5 residues processed: 132 average time/residue: 0.6381 time to fit residues: 92.9384 Evaluate side-chains 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 11 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN A 419 GLN B 411 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063581 restraints weight = 28763.089| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.06 r_work: 0.2750 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16337 Z= 0.151 Angle : 0.511 9.407 21965 Z= 0.259 Chirality : 0.039 0.165 2372 Planarity : 0.003 0.028 2627 Dihedral : 14.201 158.305 3264 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.72 % Allowed : 24.14 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.21), residues: 1788 helix: 2.52 (0.15), residues: 1184 sheet: 1.80 (0.55), residues: 48 loop : -0.39 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 271 TYR 0.013 0.001 TYR B 349 PHE 0.012 0.001 PHE A 298 TRP 0.015 0.001 TRP C 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16337) covalent geometry : angle 0.51131 / 0.26 (21965) hydrogen bonds : bond 0.03840 / 2.55 ( 930) hydrogen bonds : angle 3.46162 / 2.49 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.639 Fit side-chains REVERT: A 305 MET cc_start: 0.9061 (ttm) cc_final: 0.8779 (ttp) REVERT: A 476 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8417 (mttt) REVERT: B 234 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8664 (tm) REVERT: B 305 MET cc_start: 0.9062 (ttm) cc_final: 0.8773 (ttp) REVERT: B 476 LYS cc_start: 0.8728 (mmpt) cc_final: 0.8370 (mttt) REVERT: B 496 GLN cc_start: 0.9253 (mt0) cc_final: 0.8964 (mm-40) REVERT: C 305 MET cc_start: 0.9079 (ttm) cc_final: 0.8802 (ttp) REVERT: C 476 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8363 (mttt) REVERT: C 496 GLN cc_start: 0.9236 (mt0) cc_final: 0.8947 (mm-40) REVERT: D 476 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8362 (mttt) REVERT: D 487 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8386 (pt) REVERT: D 496 GLN cc_start: 0.9237 (mt0) cc_final: 0.8914 (mm-40) outliers start: 44 outliers final: 15 residues processed: 147 average time/residue: 0.6299 time to fit residues: 102.8015 Evaluate side-chains 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.097004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064757 restraints weight = 29095.512| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.08 r_work: 0.2774 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16337 Z= 0.111 Angle : 0.511 9.628 21965 Z= 0.256 Chirality : 0.038 0.145 2372 Planarity : 0.003 0.028 2627 Dihedral : 13.899 158.741 3264 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 25.31 % Favored : 72.72 % 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: 2.51 (0.21), residues: 1788 helix: 2.56 (0.15), residues: 1184 sheet: 1.75 (0.55), residues: 48 loop : -0.34 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.012 0.001 TYR B 349 PHE 0.009 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (16337) covalent geometry : angle 0.51091 / 0.26 (21965) hydrogen bonds : bond 0.03471 / 2.31 ( 930) hydrogen bonds : angle 3.38945 / 2.43 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9069 (ttm) cc_final: 0.8787 (ttp) REVERT: A 476 LYS cc_start: 0.8781 (mmpt) cc_final: 0.8453 (mttt) REVERT: A 590 ASP cc_start: 0.8520 (p0) cc_final: 0.8174 (p0) REVERT: B 234 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8656 (tm) REVERT: B 305 MET cc_start: 0.9078 (ttm) cc_final: 0.8790 (ttp) REVERT: B 476 LYS cc_start: 0.8732 (mmpt) cc_final: 0.8380 (mttt) REVERT: B 496 GLN cc_start: 0.9266 (mt0) cc_final: 0.8983 (mm-40) REVERT: C 305 MET cc_start: 0.9071 (ttm) cc_final: 0.8802 (ttp) REVERT: C 476 LYS cc_start: 0.8761 (mmpt) cc_final: 0.8403 (mttt) REVERT: C 496 GLN cc_start: 0.9241 (mt0) cc_final: 0.8939 (mm-40) REVERT: D 305 MET cc_start: 0.9073 (ttm) cc_final: 0.8800 (ttp) REVERT: D 476 LYS cc_start: 0.8723 (mmpt) cc_final: 0.8381 (mttt) REVERT: D 487 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8374 (pt) REVERT: D 496 GLN cc_start: 0.9241 (mt0) cc_final: 0.8937 (mm-40) REVERT: D 590 ASP cc_start: 0.8398 (p0) cc_final: 0.8049 (p0) outliers start: 32 outliers final: 7 residues processed: 138 average time/residue: 0.6438 time to fit residues: 98.3700 Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 483 CYS Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 144 optimal weight: 0.3980 chunk 167 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.061688 restraints weight = 28991.865| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.07 r_work: 0.2705 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16337 Z= 0.262 Angle : 0.605 10.030 21965 Z= 0.303 Chirality : 0.043 0.208 2372 Planarity : 0.003 0.028 2627 Dihedral : 15.071 155.883 3264 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.35 % Allowed : 24.75 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.21), residues: 1788 helix: 2.33 (0.15), residues: 1184 sheet: 1.90 (0.55), residues: 48 loop : -0.49 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 271 TYR 0.017 0.002 TYR D 349 PHE 0.015 0.002 PHE A 298 TRP 0.016 0.002 TRP A 168 HIS 0.006 0.002 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (16337) covalent geometry : angle 0.60532 / 0.30 (21965) hydrogen bonds : bond 0.04568 / 3.02 ( 930) hydrogen bonds : angle 3.69528 / 2.66 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.627 Fit side-chains REVERT: A 476 LYS cc_start: 0.8765 (mmpt) cc_final: 0.8368 (mttt) REVERT: B 234 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8689 (tm) REVERT: B 476 LYS cc_start: 0.8684 (mmpt) cc_final: 0.8310 (mttt) REVERT: B 496 GLN cc_start: 0.9222 (mt0) cc_final: 0.8904 (mm-40) REVERT: C 476 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8318 (mttt) REVERT: C 496 GLN cc_start: 0.9209 (mt0) cc_final: 0.8894 (mm-40) REVERT: D 476 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8355 (mttt) REVERT: D 487 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8410 (pt) REVERT: D 496 GLN cc_start: 0.9216 (mt0) cc_final: 0.8882 (mm-40) REVERT: D 590 ASP cc_start: 0.8455 (p0) cc_final: 0.8118 (p0) outliers start: 38 outliers final: 15 residues processed: 142 average time/residue: 0.6216 time to fit residues: 98.0251 Evaluate side-chains 126 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 CYS Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.064402 restraints weight = 28787.445| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.06 r_work: 0.2768 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16337 Z= 0.121 Angle : 0.538 10.216 21965 Z= 0.269 Chirality : 0.039 0.145 2372 Planarity : 0.003 0.028 2627 Dihedral : 14.213 158.157 3264 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.05 % Allowed : 26.05 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.21), residues: 1788 helix: 2.48 (0.15), residues: 1184 sheet: 1.79 (0.56), residues: 48 loop : -0.44 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 287 TYR 0.012 0.001 TYR A 349 PHE 0.010 0.001 PHE A 298 TRP 0.016 0.001 TRP C 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16337) covalent geometry : angle 0.53810 / 0.27 (21965) hydrogen bonds : bond 0.03547 / 2.35 ( 930) hydrogen bonds : angle 3.48100 / 2.50 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.9047 (ttm) cc_final: 0.8761 (ttp) REVERT: A 476 LYS cc_start: 0.8760 (mmpt) cc_final: 0.8385 (mttt) REVERT: A 590 ASP cc_start: 0.8565 (p0) cc_final: 0.8180 (p0) REVERT: B 234 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (tm) REVERT: B 305 MET cc_start: 0.9053 (ttm) cc_final: 0.8763 (ttp) REVERT: B 476 LYS cc_start: 0.8709 (mmpt) cc_final: 0.8345 (mttt) REVERT: B 496 GLN cc_start: 0.9266 (mt0) cc_final: 0.8975 (mm-40) REVERT: B 604 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6944 (ppp) REVERT: C 305 MET cc_start: 0.9060 (ttm) cc_final: 0.8790 (ttp) REVERT: C 476 LYS cc_start: 0.8734 (mmpt) cc_final: 0.8352 (mttt) REVERT: C 496 GLN cc_start: 0.9248 (mt0) cc_final: 0.8958 (mm-40) REVERT: C 601 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8749 (pp30) REVERT: D 476 LYS cc_start: 0.8701 (mmpt) cc_final: 0.8355 (mttt) REVERT: D 487 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8376 (pt) REVERT: D 496 GLN cc_start: 0.9238 (mt0) cc_final: 0.8868 (mm-40) REVERT: D 590 ASP cc_start: 0.8403 (p0) cc_final: 0.8091 (p0) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.6972 time to fit residues: 96.1615 Evaluate side-chains 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 483 CYS Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 CYS Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN B 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063104 restraints weight = 28806.136| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.07 r_work: 0.2737 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16337 Z= 0.170 Angle : 0.557 10.117 21965 Z= 0.279 Chirality : 0.040 0.173 2372 Planarity : 0.003 0.028 2627 Dihedral : 14.467 157.463 3264 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.79 % Allowed : 25.25 % Favored : 72.96 % 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: 2.35 (0.21), residues: 1788 helix: 2.45 (0.15), residues: 1184 sheet: 1.79 (0.56), residues: 48 loop : -0.47 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 287 TYR 0.013 0.001 TYR B 349 PHE 0.012 0.001 PHE A 298 TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (16337) covalent geometry : angle 0.55678 / 0.28 (21965) hydrogen bonds : bond 0.03982 / 2.64 ( 930) hydrogen bonds : angle 3.55123 / 2.55 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6520.95 seconds wall clock time: 111 minutes 52.97 seconds (6712.97 seconds total)