Starting phenix.real_space_refine on Fri Jul 3 22:06:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.map" model { file = "/net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpv_74534/07_2026/9zpv_74534.cif" } resolution = 2.07 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 24 5.49 5 S 76 5.16 5 C 10623 2.51 5 N 2404 2.21 5 O 2873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16006 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 3761 Chain: "B" Number of atoms: 3698 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3687 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 450, 3687 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3760 Chain: "C" Number of atoms: 3700 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Conformer: "B" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} bond proxies already assigned to first conformer: 3762 Chain: "D" Number of atoms: 3700 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Conformer: "B" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} bond proxies already assigned to first conformer: 3762 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 265 Ad-hoc single atom residues: {' K': 6} Unusual residues: {'CLR': 1, 'PCW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 6 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 298 Unusual residues: {'CLR': 1, 'PCW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'PCW:plan-2': 4, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 302 Unusual residues: {'CLR': 1, 'PCW': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 338 Unusual residues: {'CLR': 1, 'PCW': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'PCW:plan-4': 3, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 21 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 299 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG A 299 " occ=0.51 residue: pdb=" N AARG B 299 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG B 299 " occ=0.47 residue: pdb=" N AARG C 299 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG C 299 " occ=0.48 residue: pdb=" N AARG D 299 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG D 299 " occ=0.43 Time building chain proxies: 4.58, per 1000 atoms: 0.29 Number of scatterers: 16006 At special positions: 0 Unit cell: (96.3, 96.3, 121.5, 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 24 15.00 O 2873 8.00 N 2404 7.00 C 10623 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: 1.34 Conformation dependent library (CDL) restraints added in 869.0 milliseconds 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 69.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 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: 3.538A pdb=" N VAL A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.891A 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 254 removed outlier: 3.922A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.515A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.664A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.026A 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 372 through 404 WARNING: missing atoms! 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 476 removed outlier: 6.186A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 605 Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.568A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.207A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.854A 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 254 removed outlier: 3.940A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 removed outlier: 3.515A pdb=" N LEU B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.663A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.004A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 WARNING: missing atoms! 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 424 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 476 removed outlier: 6.156A pdb=" N ASP B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 588 through 605 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.540A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.203A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.878A 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 254 removed outlier: 3.981A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 removed outlier: 3.505A pdb=" N LEU C 258 " --> pdb=" O PRO C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.654A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.993A 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 476 removed outlier: 6.139A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 605 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.538A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.212A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.881A 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 254 removed outlier: 3.970A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 removed outlier: 3.526A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.700A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.006A 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 476 removed outlier: 6.187A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 Processing helix chain 'D' and resid 484 through 493 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 588 through 605 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: 6.651A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.582A 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: 6.775A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.709A 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: 6.565A pdb=" N PHE B 574 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE B 519 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 576 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 5.553A 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: 6.612A pdb=" N ILE B 565 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN B 564 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.727A 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: 6.712A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.587A 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: 6.628A pdb=" N ILE C 565 " --> pdb=" O ILE C 506 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.743A 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: 6.628A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.555A 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: 6.615A pdb=" N ILE D 565 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2764 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: 2.03 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2540 1.32 - 1.44: 4244 1.44 - 1.57: 9368 1.57 - 1.69: 48 1.69 - 1.81: 128 Bond restraints: 16328 Sorted by residual: bond pdb=" CB LYS D 553 " pdb=" CG LYS D 553 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CA LEU C 174 " pdb=" C LEU C 174 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.68e-01 bond pdb=" CA LEU B 174 " pdb=" C LEU B 174 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.33e-01 bond pdb=" C PHE C 170 " pdb=" O PHE C 170 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 7.28e-01 bond pdb=" CA LEU D 174 " pdb=" C LEU D 174 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 7.20e-01 ... (remaining 16323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 21578 1.33 - 2.65: 267 2.65 - 3.98: 67 3.98 - 5.31: 7 5.31 - 6.63: 2 Bond angle restraints: 21921 Sorted by residual: angle pdb=" CA LYS D 553 " pdb=" CB LYS D 553 " pdb=" CG LYS D 553 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " pdb=" CG TYR A 205 " ideal model delta sigma weight residual 113.90 117.95 -4.05 1.80e+00 3.09e-01 5.07e+00 angle pdb=" CA PHE B 423 " pdb=" CB PHE B 423 " pdb=" CG PHE B 423 " ideal model delta sigma weight residual 113.80 116.02 -2.22 1.00e+00 1.00e+00 4.91e+00 angle pdb=" CA PHE C 423 " pdb=" CB PHE C 423 " pdb=" CG PHE C 423 " ideal model delta sigma weight residual 113.80 116.01 -2.21 1.00e+00 1.00e+00 4.88e+00 angle pdb=" CA PHE D 423 " pdb=" CB PHE D 423 " pdb=" CG PHE D 423 " ideal model delta sigma weight residual 113.80 115.92 -2.12 1.00e+00 1.00e+00 4.49e+00 ... (remaining 21916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.79: 9148 22.79 - 45.57: 792 45.57 - 68.36: 202 68.36 - 91.15: 38 91.15 - 113.94: 4 Dihedral angle restraints: 10184 sinusoidal: 4844 harmonic: 5340 Sorted by residual: dihedral pdb=" N PCW D 702 " pdb=" C4 PCW D 702 " pdb=" C5 PCW D 702 " pdb=" O4P PCW D 702 " ideal model delta sinusoidal sigma weight residual 293.34 179.40 113.94 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" N PCW B 705 " pdb=" C4 PCW B 705 " pdb=" C5 PCW B 705 " pdb=" O4P PCW B 705 " ideal model delta sinusoidal sigma weight residual 293.34 179.89 113.45 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C33 PCW D 705 " pdb=" C31 PCW D 705 " pdb=" C32 PCW D 705 " pdb=" O2 PCW D 705 " ideal model delta sinusoidal sigma weight residual 191.83 83.65 108.18 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 10181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1496 0.029 - 0.057: 562 0.057 - 0.086: 202 0.086 - 0.115: 90 0.115 - 0.143: 10 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN A 559 " pdb=" N ASN A 559 " pdb=" C ASN A 559 " pdb=" CB ASN A 559 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE D 254 " pdb=" N ILE D 254 " pdb=" C ILE D 254 " pdb=" CB ILE D 254 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2357 not shown) Planarity restraints: 2636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 467 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE A 467 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE A 467 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 468 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 467 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C ILE D 467 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE D 467 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN D 468 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 467 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C ILE C 467 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 467 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 468 " 0.006 2.00e-02 2.50e+03 ... (remaining 2633 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 5353 2.85 - 3.42: 17298 3.42 - 4.00: 30943 4.00 - 4.57: 45346 4.57 - 5.14: 62747 Nonbonded interactions: 161687 Sorted by model distance: nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.281 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.285 3.040 nonbonded pdb=" NZ LYS B 323 " pdb=" O1P PCW B 704 " model vdw 2.288 3.120 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.304 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.308 3.040 ... (remaining 161682 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 298 or resid 300 through 316 or (resid 317 and \ (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 318 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1)) or resid 373 through 605 or (resid 703 and (name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C2 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 4 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 705 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 C \ 3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name O3 or name O31 or name O3P)) or (resid 706 \ 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 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name O11 or name O2 or name O3 or name O31 or name O3P)) or (resid 70 \ 7 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or \ name C22 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 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 C41 or name C42 or \ name O11 or name O2 or name O3 or name O31 or name O3P)))) selection = (chain 'B' and (resid 156 through 298 or resid 300 through 373 or (resid 374 and \ (name N or name CA or name C or name CB or name CG or name CD or name OE1 or na \ me OE2)) or resid 375 through 605 or (resid 703 and (name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C2 or name C3 or na \ me C31 or name C32 or name C33 or name C34 or name C35 or name C4 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 705 and (name C1 or name C11 or name C12 or name C13 or n \ ame 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 C3 \ 8 or name C39 or name O3 or name O31 or name O3P)) or (resid 706 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 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O2 or name O3 or name O31 or name O3P)) or (resid 707 and (name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C \ 17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or nam \ e C23 or name C24 or name C25 or name C26 or name C27 or name C28 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 C41 or name C42 or name C43 or name O11 or name \ O2 or name O3 or name O31 or name O3P)))) selection = (chain 'C' and (resid 156 through 298 or resid 300 through 316 or (resid 317 and \ (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 318 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1)) or resid 373 or (resid 374 and (name N or name CA or na \ me C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 375 thr \ ough 605 or (resid 703 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C4 or name O11 or name O1P or name O2 or n \ ame O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 70 \ 5 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me 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 O3 \ or name O31 or name O3P)) or (resid 706 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 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name O11 or name O2 or name O3 \ or name O31 or name O3P)) 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 C18 or name C1 \ 9 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C41 or name C42 or name C43 or name O11 or name O2 or name O3 or name O3 \ 1 or name O3P)))) selection = (chain 'D' and (resid 156 through 298 or resid 300 through 316 or (resid 317 and \ (name N or name CA or name C or name CB or name CG1 or name CG2)) or resid 318 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1)) or resid 373 or (resid 374 and (name N or name CA or na \ me C or name CB or name CG or name CD or name OE1 or name OE2)) or resid 375 thr \ ough 605 or (resid 703 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C2 or name C3 or name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C4 or name O11 or name O1P or name O2 or n \ ame O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resid 70 \ 5 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me 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 O3 \ or name O31 or name O3P)) or (resid 706 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 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name O11 or name O2 or name O3 \ or name O31 or name O3P)) or resid 707)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.320 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 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 : 0.003 0.032 16328 Z= 0.129 Angle : 0.425 6.635 21921 Z= 0.228 Chirality : 0.038 0.143 2360 Planarity : 0.003 0.035 2636 Dihedral : 17.792 113.937 6760 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.74 % Allowed : 15.79 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.20), residues: 1804 helix: 2.69 (0.15), residues: 1221 sheet: 3.18 (0.46), residues: 44 loop : 0.69 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.017 0.001 TYR C 205 PHE 0.013 0.001 PHE A 423 TRP 0.016 0.001 TRP C 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16328) covalent geometry : angle 0.42519 / 0.23 (21921) hydrogen bonds : bond 0.08359 / 5.57 ( 964) hydrogen bonds : angle 3.85423 / 2.73 ( 2764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 446 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8887 (mtpt) REVERT: B 565 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9319 (mt) REVERT: C 565 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9318 (mt) REVERT: D 565 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9290 (mt) outliers start: 12 outliers final: 5 residues processed: 97 average time/residue: 0.6704 time to fit residues: 70.9428 Evaluate side-chains 94 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.061566 restraints weight = 61845.977| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.95 r_work: 0.2635 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16328 Z= 0.110 Angle : 0.415 6.593 21921 Z= 0.223 Chirality : 0.038 0.143 2360 Planarity : 0.003 0.033 2636 Dihedral : 13.920 106.962 3181 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.04 % Allowed : 15.17 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.20), residues: 1804 helix: 2.70 (0.15), residues: 1235 sheet: 3.16 (0.60), residues: 44 loop : 0.63 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 413 TYR 0.019 0.001 TYR D 205 PHE 0.012 0.001 PHE A 423 TRP 0.015 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16328) covalent geometry : angle 0.41536 / 0.22 (21921) hydrogen bonds : bond 0.03909 / 2.53 ( 964) hydrogen bonds : angle 3.35095 / 2.39 ( 2764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: B 514 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8267 (ptt90) REVERT: B 572 ASP cc_start: 0.8770 (t0) cc_final: 0.8449 (t0) REVERT: C 451 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: D 556 LYS cc_start: 0.4905 (mptt) cc_final: 0.4312 (mptp) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 0.6808 time to fit residues: 78.3822 Evaluate side-chains 95 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 0.0040 chunk 136 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 ASN B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.059971 restraints weight = 76390.826| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.26 r_work: 0.2591 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9286 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16328 Z= 0.129 Angle : 0.424 6.346 21921 Z= 0.228 Chirality : 0.038 0.142 2360 Planarity : 0.003 0.038 2636 Dihedral : 13.796 109.648 3165 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.35 % Allowed : 14.68 % Favored : 83.97 % 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: 3.15 (0.20), residues: 1804 helix: 2.67 (0.15), residues: 1235 sheet: 3.03 (0.65), residues: 44 loop : 0.63 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.018 0.001 TYR A 205 PHE 0.014 0.001 PHE A 423 TRP 0.016 0.001 TRP A 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16328) covalent geometry : angle 0.42354 / 0.23 (21921) hydrogen bonds : bond 0.04191 / 2.71 ( 964) hydrogen bonds : angle 3.36252 / 2.40 ( 2764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 514 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (ptt90) REVERT: B 572 ASP cc_start: 0.8819 (t0) cc_final: 0.8507 (t0) REVERT: C 451 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: C 514 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8465 (ptt180) REVERT: C 572 ASP cc_start: 0.8892 (t0) cc_final: 0.8578 (t0) REVERT: D 556 LYS cc_start: 0.4930 (OUTLIER) cc_final: 0.4292 (mptp) outliers start: 22 outliers final: 10 residues processed: 108 average time/residue: 0.6866 time to fit residues: 80.9132 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060968 restraints weight = 66115.219| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.05 r_work: 0.2619 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.0487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16328 Z= 0.114 Angle : 0.409 7.916 21921 Z= 0.219 Chirality : 0.038 0.142 2360 Planarity : 0.003 0.033 2636 Dihedral : 13.549 108.568 3165 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.41 % Allowed : 14.50 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.20), residues: 1804 helix: 2.72 (0.15), residues: 1228 sheet: 2.94 (0.68), residues: 44 loop : 0.68 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.017 0.001 TYR A 205 PHE 0.012 0.001 PHE A 423 TRP 0.015 0.001 TRP A 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16328) covalent geometry : angle 0.40904 / 0.22 (21921) hydrogen bonds : bond 0.03930 / 2.54 ( 964) hydrogen bonds : angle 3.29206 / 2.36 ( 2764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 514 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8326 (ptt90) REVERT: B 572 ASP cc_start: 0.8788 (t0) cc_final: 0.8483 (t0) REVERT: C 451 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: C 514 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (ptt180) REVERT: C 572 ASP cc_start: 0.8851 (t0) cc_final: 0.8546 (t0) REVERT: D 556 LYS cc_start: 0.4910 (OUTLIER) cc_final: 0.4260 (mptp) outliers start: 23 outliers final: 9 residues processed: 110 average time/residue: 0.7132 time to fit residues: 85.2451 Evaluate side-chains 103 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN A 559 ASN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.062659 restraints weight = 68605.500| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.11 r_work: 0.2657 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9243 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16328 Z= 0.088 Angle : 0.385 6.958 21921 Z= 0.205 Chirality : 0.037 0.144 2360 Planarity : 0.003 0.026 2636 Dihedral : 13.017 103.338 3165 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.23 % Allowed : 15.05 % Favored : 83.72 % 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: 3.64 (0.20), residues: 1804 helix: 3.20 (0.15), residues: 1163 sheet: 2.78 (0.68), residues: 44 loop : 0.81 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.002 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (16328) covalent geometry : angle 0.38462 / 0.20 (21921) hydrogen bonds : bond 0.03379 / 2.19 ( 964) hydrogen bonds : angle 3.13357 / 2.25 ( 2764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.574 Fit side-chains REVERT: A 572 ASP cc_start: 0.8786 (t0) cc_final: 0.8483 (t0) REVERT: B 572 ASP cc_start: 0.8749 (t0) cc_final: 0.8448 (t0) REVERT: C 451 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8746 (mtmm) REVERT: C 514 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8428 (ptt180) REVERT: C 572 ASP cc_start: 0.8795 (t0) cc_final: 0.8499 (t0) REVERT: D 556 LYS cc_start: 0.4907 (OUTLIER) cc_final: 0.4279 (mptp) REVERT: D 572 ASP cc_start: 0.8745 (t0) cc_final: 0.8409 (t0) outliers start: 20 outliers final: 4 residues processed: 110 average time/residue: 0.7072 time to fit residues: 84.4328 Evaluate side-chains 101 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 134 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.062377 restraints weight = 77667.184| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.25 r_work: 0.2635 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16328 Z= 0.094 Angle : 0.390 6.771 21921 Z= 0.208 Chirality : 0.037 0.144 2360 Planarity : 0.003 0.027 2636 Dihedral : 12.922 104.415 3164 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.92 % Allowed : 15.36 % Favored : 83.72 % 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: 3.59 (0.20), residues: 1804 helix: 3.12 (0.15), residues: 1174 sheet: 2.75 (0.69), residues: 44 loop : 0.81 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.015 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (16328) covalent geometry : angle 0.38980 / 0.21 (21921) hydrogen bonds : bond 0.03552 / 2.30 ( 964) hydrogen bonds : angle 3.14578 / 2.25 ( 2764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.8818 (t0) cc_final: 0.8513 (t0) REVERT: B 514 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8282 (ptt90) REVERT: B 572 ASP cc_start: 0.8788 (t0) cc_final: 0.8486 (t0) REVERT: C 451 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8742 (mtmm) REVERT: C 572 ASP cc_start: 0.8851 (t0) cc_final: 0.8546 (t0) REVERT: D 556 LYS cc_start: 0.4910 (OUTLIER) cc_final: 0.4278 (mptp) REVERT: D 572 ASP cc_start: 0.8776 (t0) cc_final: 0.8446 (t0) outliers start: 15 outliers final: 3 residues processed: 107 average time/residue: 0.6566 time to fit residues: 76.4767 Evaluate side-chains 99 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 156 optimal weight: 0.0070 chunk 121 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062070 restraints weight = 74510.393| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.24 r_work: 0.2645 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9253 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16328 Z= 0.092 Angle : 0.387 6.235 21921 Z= 0.207 Chirality : 0.037 0.143 2360 Planarity : 0.003 0.026 2636 Dihedral : 12.702 103.944 3164 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.86 % Allowed : 15.42 % Favored : 83.72 % 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: 3.67 (0.20), residues: 1804 helix: 3.22 (0.15), residues: 1163 sheet: 2.69 (0.69), residues: 44 loop : 0.84 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (16328) covalent geometry : angle 0.38704 / 0.21 (21921) hydrogen bonds : bond 0.03475 / 2.25 ( 964) hydrogen bonds : angle 3.12089 / 2.24 ( 2764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.581 Fit side-chains REVERT: A 572 ASP cc_start: 0.8819 (t0) cc_final: 0.8515 (t0) REVERT: B 514 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (ptt90) REVERT: B 572 ASP cc_start: 0.8785 (t0) cc_final: 0.8490 (t0) REVERT: C 451 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8738 (mtmm) REVERT: C 514 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8432 (ptt180) REVERT: C 572 ASP cc_start: 0.8829 (t0) cc_final: 0.8536 (t0) REVERT: D 556 LYS cc_start: 0.4923 (OUTLIER) cc_final: 0.4293 (mptp) REVERT: D 572 ASP cc_start: 0.8767 (t0) cc_final: 0.8440 (t0) outliers start: 14 outliers final: 5 residues processed: 106 average time/residue: 0.6618 time to fit residues: 76.2957 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062038 restraints weight = 82621.760| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.31 r_work: 0.2620 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16328 Z= 0.103 Angle : 0.401 9.754 21921 Z= 0.214 Chirality : 0.037 0.142 2360 Planarity : 0.003 0.030 2636 Dihedral : 12.761 103.575 3164 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.49 % Allowed : 15.79 % Favored : 83.72 % 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: 3.50 (0.20), residues: 1804 helix: 3.01 (0.15), residues: 1192 sheet: 2.76 (0.70), residues: 44 loop : 0.82 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.010 0.001 PHE A 423 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (16328) covalent geometry : angle 0.40133 / 0.21 (21921) hydrogen bonds : bond 0.03729 / 2.41 ( 964) hydrogen bonds : angle 3.17605 / 2.28 ( 2764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.588 Fit side-chains REVERT: A 572 ASP cc_start: 0.8848 (t0) cc_final: 0.8537 (t0) REVERT: B 514 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (ptt90) REVERT: B 572 ASP cc_start: 0.8822 (t0) cc_final: 0.8520 (t0) REVERT: C 451 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (mtmm) REVERT: C 514 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8433 (ptt180) REVERT: C 572 ASP cc_start: 0.8874 (t0) cc_final: 0.8570 (t0) REVERT: D 556 LYS cc_start: 0.4988 (OUTLIER) cc_final: 0.4358 (mptp) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.7671 time to fit residues: 82.7064 Evaluate side-chains 103 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.062285 restraints weight = 78555.846| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.21 r_work: 0.2627 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9261 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16328 Z= 0.102 Angle : 0.399 9.263 21921 Z= 0.213 Chirality : 0.037 0.142 2360 Planarity : 0.003 0.029 2636 Dihedral : 12.740 106.224 3164 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.55 % Allowed : 15.79 % Favored : 83.66 % 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: 3.50 (0.20), residues: 1804 helix: 3.01 (0.15), residues: 1192 sheet: 2.75 (0.70), residues: 44 loop : 0.82 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.010 0.001 PHE A 423 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (16328) covalent geometry : angle 0.39923 / 0.21 (21921) hydrogen bonds : bond 0.03686 / 2.39 ( 964) hydrogen bonds : angle 3.17442 / 2.28 ( 2764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.410 Fit side-chains REVERT: A 572 ASP cc_start: 0.8839 (t0) cc_final: 0.8529 (t0) REVERT: B 514 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8317 (ptt90) REVERT: B 572 ASP cc_start: 0.8823 (t0) cc_final: 0.8519 (t0) REVERT: C 451 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (mtmm) REVERT: C 514 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8429 (ptt180) REVERT: C 572 ASP cc_start: 0.8860 (t0) cc_final: 0.8558 (t0) REVERT: D 556 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4364 (mptp) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.7569 time to fit residues: 82.5976 Evaluate side-chains 103 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 423 PHE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 423 PHE Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.0060 chunk 79 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063029 restraints weight = 53907.686| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.77 r_work: 0.2674 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9249 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16328 Z= 0.092 Angle : 0.390 9.229 21921 Z= 0.208 Chirality : 0.037 0.143 2360 Planarity : 0.003 0.026 2636 Dihedral : 12.607 103.631 3164 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.55 % Allowed : 15.66 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.20), residues: 1804 helix: 3.19 (0.15), residues: 1170 sheet: 2.70 (0.69), residues: 44 loop : 0.83 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.014 0.001 TRP B 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (16328) covalent geometry : angle 0.39019 / 0.21 (21921) hydrogen bonds : bond 0.03477 / 2.25 ( 964) hydrogen bonds : angle 3.12097 / 2.24 ( 2764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.569 Fit side-chains REVERT: A 572 ASP cc_start: 0.8761 (t0) cc_final: 0.8470 (t0) REVERT: B 514 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8252 (ptt90) REVERT: B 572 ASP cc_start: 0.8727 (t0) cc_final: 0.8437 (t0) REVERT: C 451 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8740 (mtmm) REVERT: C 514 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8398 (ptt180) REVERT: C 572 ASP cc_start: 0.8790 (t0) cc_final: 0.8496 (t0) REVERT: D 556 LYS cc_start: 0.4956 (OUTLIER) cc_final: 0.4310 (mptp) REVERT: D 572 ASP cc_start: 0.8707 (t0) cc_final: 0.8393 (t0) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.7327 time to fit residues: 79.6100 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 556 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062426 restraints weight = 86572.928| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.39 r_work: 0.2621 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9273 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16328 Z= 0.099 Angle : 0.397 9.227 21921 Z= 0.212 Chirality : 0.037 0.142 2360 Planarity : 0.003 0.028 2636 Dihedral : 12.622 104.254 3164 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.49 % Allowed : 15.66 % Favored : 83.85 % 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: 3.59 (0.20), residues: 1804 helix: 3.10 (0.15), residues: 1181 sheet: 2.74 (0.70), residues: 44 loop : 0.84 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.016 0.001 TYR A 205 PHE 0.010 0.001 PHE A 423 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 0.00216 / 0.10 (16328) covalent geometry : angle 0.39693 / 0.21 (21921) hydrogen bonds : bond 0.03621 / 2.34 ( 964) hydrogen bonds : angle 3.14653 / 2.26 ( 2764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5695.55 seconds wall clock time: 97 minutes 30.19 seconds (5850.19 seconds total)