Starting phenix.real_space_refine on Thu Feb 5 09:07:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zpv_74534/02_2026/9zpv_74534.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zpv_74534/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9zpv_74534/02_2026/9zpv_74534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zpv_74534/02_2026/9zpv_74534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zpv_74534/02_2026/9zpv_74534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zpv_74534/02_2026/9zpv_74534.map" } 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-2.0-5952/lib/python3.9/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, 271 Unusual residues: {' K': 6, 'CLR': 1, 'PCW': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 6.68, per 1000 atoms: 0.42 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: 1.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.59 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: 2.77 Time building geometry restraints manager: 1.85 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: 2.950 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.650 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 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 covalent geometry : bond 0.00292 (16328) covalent geometry : angle 0.42519 (21921) hydrogen bonds : bond 0.08359 ( 964) hydrogen bonds : angle 3.85423 ( 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 : 0.624 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: 0.7885 time to fit residues: 83.4181 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 : 0.602 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.061866 restraints weight = 61955.273| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.96 r_work: 0.2641 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 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 = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.0409 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= 0.105 Angle : 0.412 6.606 21921 Z= 0.221 Chirality : 0.038 0.143 2360 Planarity : 0.003 0.032 2636 Dihedral : 13.867 107.061 3181 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.74 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: 3.23 (0.20), residues: 1804 helix: 2.74 (0.15), residues: 1228 sheet: 3.17 (0.60), residues: 44 loop : 0.66 (0.26), residues: 532 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 0.011 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 covalent geometry : bond 0.00228 (16328) covalent geometry : angle 0.41178 (21921) hydrogen bonds : bond 0.03823 ( 964) hydrogen bonds : angle 3.33552 ( 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 107 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8779 (t0) cc_final: 0.8457 (t0) REVERT: C 451 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8762 (mtmm) REVERT: C 572 ASP cc_start: 0.8863 (t0) cc_final: 0.8537 (t0) REVERT: D 556 LYS cc_start: 0.4922 (mptt) cc_final: 0.4329 (mptp) outliers start: 15 outliers final: 6 residues processed: 106 average time/residue: 0.7976 time to fit residues: 91.8727 Evaluate side-chains 96 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 423 PHE Chi-restraints excluded: chain C residue 329 ASN 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: 7.9990 chunk 136 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3306 r_free = 0.3306 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.059027 restraints weight = 74634.285| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.21 r_work: 0.2571 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16328 Z= 0.171 Angle : 0.454 6.446 21921 Z= 0.245 Chirality : 0.039 0.143 2360 Planarity : 0.003 0.048 2636 Dihedral : 14.189 113.789 3165 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.41 % Allowed : 14.62 % 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: 3.20 (0.20), residues: 1804 helix: 2.69 (0.15), residues: 1219 sheet: 3.08 (0.64), residues: 44 loop : 0.77 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.018 0.001 TYR D 349 PHE 0.017 0.001 PHE A 423 TRP 0.016 0.001 TRP A 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00397 (16328) covalent geometry : angle 0.45406 (21921) hydrogen bonds : bond 0.04690 ( 964) hydrogen bonds : angle 3.48917 ( 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 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: B 514 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (ptt90) REVERT: C 451 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8776 (mtmm) REVERT: C 514 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8447 (ptt180) REVERT: D 556 LYS cc_start: 0.4962 (OUTLIER) cc_final: 0.4298 (mptp) outliers start: 23 outliers final: 9 residues processed: 107 average time/residue: 0.7897 time to fit residues: 91.6679 Evaluate side-chains 98 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 129 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3346 r_free = 0.3346 target = 0.086037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061820 restraints weight = 66454.960| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.04 r_work: 0.2641 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16328 Z= 0.096 Angle : 0.397 8.249 21921 Z= 0.211 Chirality : 0.037 0.145 2360 Planarity : 0.003 0.027 2636 Dihedral : 13.478 107.958 3165 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.35 % Allowed : 14.62 % Favored : 84.03 % 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: 3.45 (0.20), residues: 1804 helix: 2.98 (0.15), residues: 1195 sheet: 2.87 (0.67), residues: 44 loop : 0.74 (0.26), residues: 565 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 0.010 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00206 (16328) covalent geometry : angle 0.39653 (21921) hydrogen bonds : bond 0.03598 ( 964) hydrogen bonds : angle 3.22422 ( 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 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 572 ASP cc_start: 0.8790 (t0) cc_final: 0.8479 (t0) REVERT: B 514 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8359 (ptt90) REVERT: B 572 ASP cc_start: 0.8776 (t0) cc_final: 0.8471 (t0) REVERT: C 451 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (mtmm) REVERT: C 514 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8430 (ptt180) REVERT: C 572 ASP cc_start: 0.8832 (t0) cc_final: 0.8521 (t0) REVERT: D 556 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4269 (mptp) outliers start: 22 outliers final: 6 residues processed: 110 average time/residue: 0.7681 time to fit residues: 91.9354 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 451 LYS Chi-restraints excluded: chain C residue 514 ARG 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: 0.3980 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.086559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062309 restraints weight = 67617.002| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.07 r_work: 0.2653 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 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 = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.0649 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= 0.092 Angle : 0.390 7.413 21921 Z= 0.208 Chirality : 0.037 0.146 2360 Planarity : 0.003 0.027 2636 Dihedral : 13.038 105.402 3165 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.74 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: 3.60 (0.20), residues: 1804 helix: 3.14 (0.15), residues: 1177 sheet: 2.74 (0.67), residues: 44 loop : 0.81 (0.25), residues: 583 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 312 Details of bonding type rmsd covalent geometry : bond 0.00196 (16328) covalent geometry : angle 0.38961 (21921) hydrogen bonds : bond 0.03497 ( 964) hydrogen bonds : angle 3.14391 ( 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 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.628 Fit side-chains REVERT: A 572 ASP cc_start: 0.8789 (t0) cc_final: 0.8492 (t0) REVERT: B 514 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8336 (ptt90) REVERT: B 572 ASP cc_start: 0.8755 (t0) cc_final: 0.8453 (t0) REVERT: C 451 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: C 572 ASP cc_start: 0.8801 (t0) cc_final: 0.8507 (t0) REVERT: D 556 LYS cc_start: 0.4949 (OUTLIER) cc_final: 0.4298 (mptp) REVERT: D 572 ASP cc_start: 0.8755 (t0) cc_final: 0.8425 (t0) outliers start: 15 outliers final: 4 residues processed: 108 average time/residue: 0.7367 time to fit residues: 86.6176 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 122 optimal weight: 0.0570 chunk 121 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 chunk 27 optimal weight: 0.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 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 = 0.3361 r_free = 0.3361 target = 0.086855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.063025 restraints weight = 77770.781| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.23 r_work: 0.2651 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 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 = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0718 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= 0.088 Angle : 0.385 6.966 21921 Z= 0.205 Chirality : 0.037 0.144 2360 Planarity : 0.003 0.026 2636 Dihedral : 12.842 103.371 3165 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.98 % Allowed : 15.05 % 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: 3.68 (0.20), residues: 1804 helix: 3.23 (0.15), residues: 1163 sheet: 2.71 (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 D 413 TYR 0.015 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 covalent geometry : bond 0.00187 (16328) covalent geometry : angle 0.38489 (21921) hydrogen bonds : bond 0.03400 ( 964) hydrogen bonds : angle 3.10501 ( 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 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.494 Fit side-chains REVERT: A 572 ASP cc_start: 0.8798 (t0) cc_final: 0.8496 (t0) REVERT: B 514 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: B 572 ASP cc_start: 0.8775 (t0) cc_final: 0.8477 (t0) REVERT: C 451 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8741 (mtmm) REVERT: C 514 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8432 (ptt180) REVERT: C 572 ASP cc_start: 0.8805 (t0) cc_final: 0.8515 (t0) REVERT: D 556 LYS cc_start: 0.4944 (OUTLIER) cc_final: 0.4297 (mptp) REVERT: D 572 ASP cc_start: 0.8753 (t0) cc_final: 0.8425 (t0) outliers start: 16 outliers final: 4 residues processed: 108 average time/residue: 0.7929 time to fit residues: 92.7162 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 156 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 63 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063930 restraints weight = 74734.138| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.19 r_work: 0.2673 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 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 = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.0847 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= 0.083 Angle : 0.379 6.731 21921 Z= 0.202 Chirality : 0.037 0.144 2360 Planarity : 0.003 0.026 2636 Dihedral : 12.537 101.256 3165 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.49 % Allowed : 15.72 % 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: 3.72 (0.20), residues: 1804 helix: 3.25 (0.15), residues: 1163 sheet: 2.71 (0.69), residues: 44 loop : 0.87 (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 B 574 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00174 (16328) covalent geometry : angle 0.37893 (21921) hydrogen bonds : bond 0.03224 ( 964) hydrogen bonds : angle 3.04575 ( 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 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.638 Fit side-chains REVERT: A 572 ASP cc_start: 0.8765 (t0) cc_final: 0.8462 (t0) REVERT: B 514 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8287 (ptt90) REVERT: B 572 ASP cc_start: 0.8760 (t0) cc_final: 0.8462 (t0) REVERT: C 451 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8732 (mtmm) REVERT: C 514 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8429 (ptt180) REVERT: C 572 ASP cc_start: 0.8789 (t0) cc_final: 0.8502 (t0) REVERT: D 556 LYS cc_start: 0.4893 (OUTLIER) cc_final: 0.4221 (mptp) REVERT: D 572 ASP cc_start: 0.8716 (t0) cc_final: 0.8402 (t0) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.8646 time to fit residues: 93.7729 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.6980 chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 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 = 0.3364 r_free = 0.3364 target = 0.087029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063279 restraints weight = 83203.634| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.31 r_work: 0.2645 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.0796 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= 0.089 Angle : 0.385 6.518 21921 Z= 0.206 Chirality : 0.037 0.143 2360 Planarity : 0.003 0.026 2636 Dihedral : 12.463 101.214 3164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.49 % Allowed : 15.48 % Favored : 84.03 % 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: 3.72 (0.20), residues: 1804 helix: 3.24 (0.15), residues: 1163 sheet: 2.76 (0.70), residues: 44 loop : 0.88 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.015 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00189 (16328) covalent geometry : angle 0.38520 (21921) hydrogen bonds : bond 0.03408 ( 964) hydrogen bonds : angle 3.07848 ( 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 101 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.775 Fit side-chains REVERT: A 572 ASP cc_start: 0.8817 (t0) cc_final: 0.8530 (t0) REVERT: B 514 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (ptt90) REVERT: B 572 ASP cc_start: 0.8804 (t0) cc_final: 0.8507 (t0) REVERT: C 451 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8760 (mtmm) REVERT: C 514 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8417 (ptt180) REVERT: C 572 ASP cc_start: 0.8828 (t0) cc_final: 0.8550 (t0) REVERT: D 556 LYS cc_start: 0.4908 (OUTLIER) cc_final: 0.4217 (mptp) REVERT: D 572 ASP cc_start: 0.8778 (t0) cc_final: 0.8455 (t0) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 0.7762 time to fit residues: 84.3557 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.062802 restraints weight = 79153.986| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.24 r_work: 0.2645 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.0762 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= 0.093 Angle : 0.390 6.332 21921 Z= 0.209 Chirality : 0.037 0.143 2360 Planarity : 0.003 0.027 2636 Dihedral : 12.465 102.296 3164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.49 % Allowed : 15.54 % 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: 3.70 (0.20), residues: 1804 helix: 3.23 (0.15), residues: 1163 sheet: 2.77 (0.70), residues: 44 loop : 0.89 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.015 0.001 TYR A 205 PHE 0.009 0.001 PHE A 298 TRP 0.014 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00201 (16328) covalent geometry : angle 0.38977 (21921) hydrogen bonds : bond 0.03516 ( 964) hydrogen bonds : angle 3.10328 ( 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: 8 poor density : 93 time to evaluate : 0.575 Fit side-chains REVERT: A 572 ASP cc_start: 0.8816 (t0) cc_final: 0.8519 (t0) REVERT: B 514 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8281 (ptt90) REVERT: B 572 ASP cc_start: 0.8763 (t0) cc_final: 0.8484 (t0) REVERT: C 451 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8736 (mtmm) REVERT: C 514 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8414 (ptt180) REVERT: C 572 ASP cc_start: 0.8813 (t0) cc_final: 0.8524 (t0) REVERT: D 556 LYS cc_start: 0.4949 (OUTLIER) cc_final: 0.4296 (mptp) REVERT: D 572 ASP cc_start: 0.8770 (t0) cc_final: 0.8439 (t0) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.8183 time to fit residues: 88.8200 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 : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 107 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 152 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 146 optimal weight: 0.0030 chunk 97 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.066221 restraints weight = 54526.577| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.77 r_work: 0.2751 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.031 16328 Z= 0.075 Angle : 0.369 6.066 21921 Z= 0.195 Chirality : 0.036 0.147 2360 Planarity : 0.003 0.035 2636 Dihedral : 12.061 97.040 3164 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.25 % Allowed : 15.79 % 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: 3.78 (0.20), residues: 1804 helix: 3.29 (0.15), residues: 1163 sheet: 2.61 (0.68), residues: 44 loop : 0.91 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 218 TYR 0.015 0.001 TYR A 205 PHE 0.010 0.001 PHE B 574 TRP 0.014 0.001 TRP A 168 HIS 0.001 0.000 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00149 (16328) covalent geometry : angle 0.36871 (21921) hydrogen bonds : bond 0.02802 ( 964) hydrogen bonds : angle 2.94081 ( 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 99 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.684 Fit side-chains REVERT: A 572 ASP cc_start: 0.8666 (t0) cc_final: 0.8394 (t0) REVERT: B 572 ASP cc_start: 0.8689 (t0) cc_final: 0.8387 (t0) REVERT: C 514 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8394 (ptt180) REVERT: C 572 ASP cc_start: 0.8674 (t0) cc_final: 0.8408 (t0) REVERT: D 556 LYS cc_start: 0.4987 (mptt) cc_final: 0.4355 (mptp) REVERT: D 572 ASP cc_start: 0.8622 (t0) cc_final: 0.8341 (t0) outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.8566 time to fit residues: 91.4138 Evaluate side-chains 96 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain C residue 514 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 0.0770 chunk 81 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062046 restraints weight = 86237.886| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.38 r_work: 0.2621 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- 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 = 0.40 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 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.0768 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= 0.109 Angle : 0.405 6.374 21921 Z= 0.217 Chirality : 0.037 0.143 2360 Planarity : 0.003 0.030 2636 Dihedral : 12.406 101.606 3164 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.25 % Allowed : 15.72 % Favored : 84.03 % 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: 3.61 (0.20), residues: 1804 helix: 3.09 (0.15), residues: 1185 sheet: 2.70 (0.69), residues: 44 loop : 0.89 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 424 TYR 0.016 0.001 TYR A 205 PHE 0.022 0.001 PHE A 423 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00243 (16328) covalent geometry : angle 0.40454 (21921) hydrogen bonds : bond 0.03808 ( 964) hydrogen bonds : angle 3.14645 ( 2764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6629.02 seconds wall clock time: 113 minutes 26.74 seconds (6806.74 seconds total)