Starting phenix.real_space_refine on Sat Sep 12 11:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ubs_20714/09_2026/6ubs_20714.map" } resolution = 3.33 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 100 5.16 5 C 9950 2.51 5 N 2440 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "D" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "E" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2949 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 16, 'TRANS': 345} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 1, 'PX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {'PIO': 1, 'PX4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'PIO': 1, 'PX4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15270 At special positions: 0 Unit cell: (99.828, 100.89, 139.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 10 15.00 O 2770 8.00 N 2440 7.00 C 9950 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN D 62 " " NAG J 1 " - " ASN E 62 " Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 479.2 milliseconds 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 41.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.747A pdb=" N ASP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.502A pdb=" N SER A 116 " --> pdb=" O MET A 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 117' Processing helix chain 'A' and resid 168 through 171 removed outlier: 3.579A pdb=" N MET A 171 " --> pdb=" O ASN A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 272 through 293 Processing helix chain 'A' and resid 305 through 341 removed outlier: 3.949A pdb=" N ILE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 443 removed outlier: 3.851A pdb=" N MET A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.709A pdb=" N PHE A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.746A pdb=" N ASP B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.503A pdb=" N SER B 116 " --> pdb=" O MET B 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 117 " --> pdb=" O LEU B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 117' Processing helix chain 'B' and resid 168 through 171 removed outlier: 3.578A pdb=" N MET B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 272 through 293 Processing helix chain 'B' and resid 305 through 341 removed outlier: 3.949A pdb=" N ILE B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 443 removed outlier: 3.850A pdb=" N MET B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.708A pdb=" N PHE B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.746A pdb=" N ASP C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.504A pdb=" N SER C 116 " --> pdb=" O MET C 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 117 " --> pdb=" O LEU C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 113 through 117' Processing helix chain 'C' and resid 168 through 171 removed outlier: 3.578A pdb=" N MET C 171 " --> pdb=" O ASN C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 252 through 263 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 272 through 293 Processing helix chain 'C' and resid 305 through 341 removed outlier: 3.948A pdb=" N ILE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 443 removed outlier: 3.851A pdb=" N MET C 399 " --> pdb=" O THR C 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.708A pdb=" N PHE C 422 " --> pdb=" O PHE C 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.746A pdb=" N ASP D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.503A pdb=" N SER D 116 " --> pdb=" O MET D 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 117 " --> pdb=" O LEU D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 117' Processing helix chain 'D' and resid 168 through 171 removed outlier: 3.579A pdb=" N MET D 171 " --> pdb=" O ASN D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 171' Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 272 through 293 Processing helix chain 'D' and resid 305 through 341 removed outlier: 3.949A pdb=" N ILE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 443 removed outlier: 3.850A pdb=" N MET D 399 " --> pdb=" O THR D 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.709A pdb=" N PHE D 422 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.747A pdb=" N ASP E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.503A pdb=" N SER E 116 " --> pdb=" O MET E 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 117 " --> pdb=" O LEU E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 113 through 117' Processing helix chain 'E' and resid 168 through 171 removed outlier: 3.579A pdb=" N MET E 171 " --> pdb=" O ASN E 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 171' Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 272 through 293 Processing helix chain 'E' and resid 305 through 341 removed outlier: 3.948A pdb=" N ILE E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 443 removed outlier: 3.851A pdb=" N MET E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Proline residue: E 419 - end of helix removed outlier: 3.708A pdb=" N PHE E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 436 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 441 " --> pdb=" O ARG E 437 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 443 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.516A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 191 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.787A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLN A 201 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE A 234 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 182 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 232 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE A 234 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 182 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 232 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 4.515A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 191 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.788A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLN B 201 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 67 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE B 234 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 182 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR B 232 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE B 234 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 182 " --> pdb=" O THR B 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR B 232 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 4.515A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 191 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.788A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLN C 201 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE C 234 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER C 182 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE C 234 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER C 182 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 108 removed outlier: 4.516A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 191 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.787A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE D 234 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER D 182 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 232 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE D 234 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER D 182 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 232 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 107 through 108 removed outlier: 4.516A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 191 " --> pdb=" O VAL E 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 127 through 131 removed outlier: 6.787A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLN E 201 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE E 67 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE E 234 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER E 182 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 232 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.670A pdb=" N ILE E 234 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER E 182 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR E 232 " --> pdb=" O SER E 182 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2055 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: 2.31 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2370 1.31 - 1.44: 4282 1.44 - 1.56: 8768 1.56 - 1.69: 30 1.69 - 1.82: 170 Bond restraints: 15620 Sorted by residual: bond pdb=" C9 PX4 D 601 " pdb=" O5 PX4 D 601 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 C 601 " pdb=" O5 PX4 C 601 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 E 902 " pdb=" O5 PX4 E 902 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C9 PX4 B 603 " pdb=" O5 PX4 B 603 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C9 PX4 C 605 " pdb=" O5 PX4 C 605 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 20737 3.35 - 6.70: 303 6.70 - 10.05: 40 10.05 - 13.39: 10 13.39 - 16.74: 5 Bond angle restraints: 21095 Sorted by residual: angle pdb=" O3 PX4 D 605 " pdb=" P1 PX4 D 605 " pdb=" O4 PX4 D 605 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 C 605 " pdb=" P1 PX4 C 605 " pdb=" O4 PX4 C 605 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 E 901 " pdb=" P1 PX4 E 901 " pdb=" O4 PX4 E 901 " ideal model delta sigma weight residual 93.64 110.38 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 B 603 " pdb=" P1 PX4 B 603 " pdb=" O4 PX4 B 603 " ideal model delta sigma weight residual 93.64 110.36 -16.72 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O3 PX4 B 606 " pdb=" P1 PX4 B 606 " pdb=" O4 PX4 B 606 " ideal model delta sigma weight residual 93.64 110.36 -16.72 3.00e+00 1.11e-01 3.11e+01 ... (remaining 21090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8006 16.19 - 32.38: 879 32.38 - 48.57: 285 48.57 - 64.76: 70 64.76 - 80.95: 10 Dihedral angle restraints: 9250 sinusoidal: 3895 harmonic: 5355 Sorted by residual: dihedral pdb=" CA GLU C 181 " pdb=" C GLU C 181 " pdb=" N SER C 182 " pdb=" CA SER C 182 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU B 181 " pdb=" C GLU B 181 " pdb=" N SER B 182 " pdb=" CA SER B 182 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU D 181 " pdb=" C GLU D 181 " pdb=" N SER D 182 " pdb=" CA SER D 182 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 9247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1586 0.046 - 0.093: 523 0.093 - 0.139: 178 0.139 - 0.186: 48 0.186 - 0.232: 20 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 62 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2352 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 411 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ASP E 411 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP E 411 " -0.026 2.00e-02 2.50e+03 pdb=" N THR E 412 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 411 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ASP D 411 " 0.069 2.00e-02 2.50e+03 pdb=" O ASP D 411 " -0.026 2.00e-02 2.50e+03 pdb=" N THR D 412 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 411 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ASP C 411 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP C 411 " 0.026 2.00e-02 2.50e+03 pdb=" N THR C 412 " 0.023 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1097 2.74 - 3.28: 14617 3.28 - 3.82: 24106 3.82 - 4.36: 28930 4.36 - 4.90: 49270 Nonbonded interactions: 118020 Sorted by model distance: nonbonded pdb=" O GLY D 278 " pdb=" OG1 THR D 282 " model vdw 2.194 3.040 nonbonded pdb=" O GLY C 278 " pdb=" OG1 THR C 282 " model vdw 2.194 3.040 nonbonded pdb=" O GLY B 278 " pdb=" OG1 THR B 282 " model vdw 2.194 3.040 nonbonded pdb=" O GLY A 278 " pdb=" OG1 THR A 282 " model vdw 2.195 3.040 nonbonded pdb=" O GLY E 278 " pdb=" OG1 THR E 282 " model vdw 2.195 3.040 ... (remaining 118015 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 31 through 601) selection = (chain 'B' and resid 31 through 601) selection = (chain 'C' and resid 31 through 601) selection = (chain 'D' and resid 31 through 601) selection = (chain 'E' and (resid 31 through 444 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C6 or name C7 or name C8 or name C9 or name O4 \ or name O5 or name O6 or name O7 or name O8 )))) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.007 0.104 15630 Z= 0.337 Angle : 1.064 16.743 21125 Z= 0.510 Chirality : 0.056 0.232 2355 Planarity : 0.008 0.044 2600 Dihedral : 15.358 80.954 5770 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.22 % Allowed : 11.87 % Favored : 86.91 % 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: -4.10 (0.16), residues: 1790 helix: -3.28 (0.14), residues: 600 sheet: -1.67 (0.23), residues: 460 loop : -2.74 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.017 0.002 TYR C 433 PHE 0.018 0.001 PHE B 319 TRP 0.018 0.002 TRP C 263 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.34 (15620) covalent geometry : angle 1.03901 / 0.50 (21095) hydrogen bonds : bond 0.14377 / 9.71 ( 665) hydrogen bonds : angle 7.57906 / 5.18 ( 2055) link_BETA1-4 : bond 0.00218 / 0.13 ( 5) link_BETA1-4 : angle 5.03950 / 2.71 ( 15) link_NAG-ASN : bond 0.00612 / 0.36 ( 5) link_NAG-ASN : angle 7.21760 / 4.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 258 ILE cc_start: 0.9350 (pt) cc_final: 0.8671 (pt) REVERT: D 258 ILE cc_start: 0.9414 (pt) cc_final: 0.8775 (pt) outliers start: 20 outliers final: 8 residues processed: 284 average time/residue: 0.0953 time to fit residues: 43.3880 Evaluate side-chains 170 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 290 GLN B 70 ASN B 290 GLN D 70 ASN D 290 GLN E 290 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069568 restraints weight = 39625.435| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.32 r_work: 0.2936 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15630 Z= 0.127 Angle : 0.627 7.295 21125 Z= 0.321 Chirality : 0.045 0.165 2355 Planarity : 0.004 0.026 2600 Dihedral : 10.462 56.977 2178 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.94 % Allowed : 13.27 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.18), residues: 1790 helix: -0.92 (0.18), residues: 660 sheet: -0.86 (0.25), residues: 435 loop : -2.49 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 276 TYR 0.014 0.001 TYR D 433 PHE 0.021 0.001 PHE D 319 TRP 0.011 0.001 TRP B 92 HIS 0.003 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (15620) covalent geometry : angle 0.61069 / 0.32 (21095) hydrogen bonds : bond 0.04430 / 2.98 ( 665) hydrogen bonds : angle 5.16687 / 3.59 ( 2055) link_BETA1-4 : bond 0.00435 / 0.25 ( 5) link_BETA1-4 : angle 3.03379 / 1.62 ( 15) link_NAG-ASN : bond 0.00172 / 0.10 ( 5) link_NAG-ASN : angle 4.48915 / 2.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7513 (p0) REVERT: A 187 MET cc_start: 0.9141 (mmm) cc_final: 0.8824 (tpt) REVERT: B 121 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7599 (p0) REVERT: C 121 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7146 (p0) REVERT: D 121 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7905 (p0) REVERT: D 244 MET cc_start: 0.8629 (ttp) cc_final: 0.8407 (ttp) REVERT: E 121 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7904 (p0) REVERT: E 187 MET cc_start: 0.9150 (mmm) cc_final: 0.8777 (tpt) outliers start: 48 outliers final: 25 residues processed: 203 average time/residue: 0.0849 time to fit residues: 29.2150 Evaluate side-chains 168 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 0.0270 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062927 restraints weight = 40718.544| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.44 r_work: 0.2790 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15630 Z= 0.243 Angle : 0.707 8.167 21125 Z= 0.365 Chirality : 0.048 0.184 2355 Planarity : 0.004 0.031 2600 Dihedral : 9.559 59.451 2177 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.98 % Allowed : 14.80 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1790 helix: 0.41 (0.20), residues: 660 sheet: -0.26 (0.26), residues: 430 loop : -2.07 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 400 TYR 0.026 0.002 TYR E 325 PHE 0.046 0.002 PHE D 319 TRP 0.015 0.002 TRP D 267 HIS 0.013 0.002 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (15620) covalent geometry : angle 0.68389 / 0.36 (21095) hydrogen bonds : bond 0.04905 / 3.34 ( 665) hydrogen bonds : angle 4.71377 / 3.28 ( 2055) link_BETA1-4 : bond 0.00496 / 0.26 ( 5) link_BETA1-4 : angle 3.32873 / 1.70 ( 15) link_NAG-ASN : bond 0.00384 / 0.22 ( 5) link_NAG-ASN : angle 5.85295 / 3.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 115 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9147 (mmm) cc_final: 0.8888 (mmm) REVERT: A 244 MET cc_start: 0.9013 (ttp) cc_final: 0.8703 (ttp) REVERT: A 323 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9088 (mm) REVERT: B 121 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (p0) REVERT: C 42 MET cc_start: 0.8894 (mpp) cc_final: 0.8687 (ptp) REVERT: C 121 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (p0) REVERT: C 323 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9201 (mm) REVERT: D 244 MET cc_start: 0.8552 (ttp) cc_final: 0.8260 (ttp) REVERT: E 42 MET cc_start: 0.8763 (mpp) cc_final: 0.8483 (ptp) REVERT: E 187 MET cc_start: 0.9123 (mmm) cc_final: 0.8898 (mmm) outliers start: 65 outliers final: 29 residues processed: 163 average time/residue: 0.0852 time to fit residues: 23.5085 Evaluate side-chains 138 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 144 optimal weight: 0.0370 chunk 157 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.065933 restraints weight = 39942.602| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.53 r_work: 0.2896 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15630 Z= 0.111 Angle : 0.592 7.473 21125 Z= 0.301 Chirality : 0.044 0.167 2355 Planarity : 0.003 0.042 2600 Dihedral : 9.077 58.610 2175 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.20 % Allowed : 16.33 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1790 helix: 0.81 (0.20), residues: 665 sheet: -0.09 (0.26), residues: 430 loop : -1.93 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.015 0.001 TYR D 325 PHE 0.015 0.001 PHE D 319 TRP 0.008 0.001 TRP A 267 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15620) covalent geometry : angle 0.57466 / 0.30 (21095) hydrogen bonds : bond 0.03616 / 2.46 ( 665) hydrogen bonds : angle 4.26406 / 2.96 ( 2055) link_BETA1-4 : bond 0.00542 / 0.31 ( 5) link_BETA1-4 : angle 3.24851 / 1.76 ( 15) link_NAG-ASN : bond 0.00333 / 0.20 ( 5) link_NAG-ASN : angle 4.32190 / 2.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8582 (ptm) cc_final: 0.8305 (ptm) REVERT: A 187 MET cc_start: 0.9186 (mmm) cc_final: 0.8905 (mmm) REVERT: A 323 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.8992 (mm) REVERT: B 121 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (p0) REVERT: C 121 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7963 (p0) REVERT: C 187 MET cc_start: 0.9172 (tpp) cc_final: 0.8462 (mpp) REVERT: C 323 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9109 (mm) REVERT: D 113 MET cc_start: 0.8944 (pmm) cc_final: 0.8563 (pmm) REVERT: D 187 MET cc_start: 0.9094 (mmm) cc_final: 0.8877 (tpt) REVERT: D 244 MET cc_start: 0.8530 (ttp) cc_final: 0.8150 (ttp) REVERT: D 323 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9093 (mm) REVERT: E 134 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8492 (tp30) REVERT: E 187 MET cc_start: 0.9140 (mmm) cc_final: 0.8857 (mmm) outliers start: 36 outliers final: 24 residues processed: 141 average time/residue: 0.0850 time to fit residues: 20.1290 Evaluate side-chains 139 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.062165 restraints weight = 40390.829| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.47 r_work: 0.2753 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15630 Z= 0.196 Angle : 0.635 8.309 21125 Z= 0.322 Chirality : 0.046 0.190 2355 Planarity : 0.004 0.026 2600 Dihedral : 8.760 58.820 2175 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.81 % Allowed : 17.43 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1790 helix: 1.09 (0.21), residues: 665 sheet: 0.02 (0.25), residues: 430 loop : -1.90 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 406 TYR 0.021 0.002 TYR D 325 PHE 0.026 0.001 PHE D 319 TRP 0.010 0.001 TRP B 92 HIS 0.005 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (15620) covalent geometry : angle 0.61519 / 0.32 (21095) hydrogen bonds : bond 0.04009 / 2.70 ( 665) hydrogen bonds : angle 4.35070 / 3.02 ( 2055) link_BETA1-4 : bond 0.00388 / 0.23 ( 5) link_BETA1-4 : angle 3.23118 / 1.68 ( 15) link_NAG-ASN : bond 0.00275 / 0.16 ( 5) link_NAG-ASN : angle 5.10454 / 3.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9163 (mmm) cc_final: 0.8829 (mmm) REVERT: A 323 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9093 (mm) REVERT: B 121 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8395 (p0) REVERT: B 187 MET cc_start: 0.9025 (mmm) cc_final: 0.8740 (mmm) REVERT: C 121 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8224 (p0) REVERT: C 134 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8229 (tp30) REVERT: C 187 MET cc_start: 0.9252 (tpp) cc_final: 0.8417 (mpp) REVERT: D 244 MET cc_start: 0.8632 (ttp) cc_final: 0.8329 (ttp) REVERT: D 323 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9209 (mm) REVERT: E 134 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8341 (tp30) REVERT: E 187 MET cc_start: 0.9140 (mmm) cc_final: 0.8760 (mmm) outliers start: 46 outliers final: 32 residues processed: 138 average time/residue: 0.0930 time to fit residues: 21.4447 Evaluate side-chains 140 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.064255 restraints weight = 39754.460| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.45 r_work: 0.2816 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15630 Z= 0.106 Angle : 0.567 7.436 21125 Z= 0.286 Chirality : 0.044 0.181 2355 Planarity : 0.003 0.025 2600 Dihedral : 8.372 58.312 2175 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.20 % Allowed : 17.74 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1790 helix: 1.27 (0.21), residues: 660 sheet: -0.03 (0.25), residues: 460 loop : -1.76 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 276 TYR 0.015 0.001 TYR D 325 PHE 0.020 0.001 PHE C 319 TRP 0.007 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15620) covalent geometry : angle 0.54908 / 0.28 (21095) hydrogen bonds : bond 0.03428 / 2.32 ( 665) hydrogen bonds : angle 4.10170 / 2.83 ( 2055) link_BETA1-4 : bond 0.00576 / 0.31 ( 5) link_BETA1-4 : angle 3.15741 / 1.71 ( 15) link_NAG-ASN : bond 0.00335 / 0.20 ( 5) link_NAG-ASN : angle 4.34286 / 2.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8627 (ptm) cc_final: 0.8305 (ptm) REVERT: A 187 MET cc_start: 0.9191 (mmm) cc_final: 0.8833 (mmm) REVERT: A 323 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 121 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8238 (p0) REVERT: B 187 MET cc_start: 0.9033 (mmm) cc_final: 0.8664 (mmm) REVERT: C 80 MET cc_start: 0.9179 (mmm) cc_final: 0.8926 (mmm) REVERT: C 121 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8040 (p0) REVERT: C 134 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8138 (tp30) REVERT: D 164 MET cc_start: 0.9417 (mtp) cc_final: 0.9147 (mtt) REVERT: D 244 MET cc_start: 0.8632 (ttp) cc_final: 0.8304 (ttp) REVERT: D 323 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9154 (mm) REVERT: E 134 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8373 (tp30) outliers start: 36 outliers final: 26 residues processed: 135 average time/residue: 0.0905 time to fit residues: 20.5382 Evaluate side-chains 137 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.062059 restraints weight = 40400.758| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.45 r_work: 0.2755 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15630 Z= 0.187 Angle : 0.604 7.702 21125 Z= 0.304 Chirality : 0.045 0.161 2355 Planarity : 0.003 0.026 2600 Dihedral : 8.219 58.355 2175 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.75 % Allowed : 17.37 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1790 helix: 1.35 (0.21), residues: 660 sheet: 0.24 (0.25), residues: 430 loop : -1.84 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 437 TYR 0.020 0.002 TYR D 325 PHE 0.016 0.001 PHE E 72 TRP 0.009 0.001 TRP E 92 HIS 0.003 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (15620) covalent geometry : angle 0.58508 / 0.30 (21095) hydrogen bonds : bond 0.03735 / 2.51 ( 665) hydrogen bonds : angle 4.22496 / 2.93 ( 2055) link_BETA1-4 : bond 0.00431 / 0.25 ( 5) link_BETA1-4 : angle 3.17613 / 1.66 ( 15) link_NAG-ASN : bond 0.00096 / 0.05 ( 5) link_NAG-ASN : angle 4.76222 / 2.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9134 (mm) REVERT: B 121 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8386 (p0) REVERT: B 187 MET cc_start: 0.9045 (mmm) cc_final: 0.8713 (mmm) REVERT: C 80 MET cc_start: 0.9233 (mmm) cc_final: 0.8884 (mtm) REVERT: C 121 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8243 (p0) REVERT: C 134 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8204 (tp30) REVERT: E 134 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8363 (tp30) outliers start: 45 outliers final: 32 residues processed: 135 average time/residue: 0.0905 time to fit residues: 20.5331 Evaluate side-chains 133 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 141 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063918 restraints weight = 40151.324| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.47 r_work: 0.2801 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15630 Z= 0.109 Angle : 0.562 7.859 21125 Z= 0.282 Chirality : 0.043 0.150 2355 Planarity : 0.003 0.025 2600 Dihedral : 7.929 56.660 2175 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.39 % Allowed : 18.04 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1790 helix: 1.43 (0.21), residues: 660 sheet: 0.11 (0.25), residues: 460 loop : -1.75 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 276 TYR 0.017 0.001 TYR D 325 PHE 0.013 0.001 PHE C 319 TRP 0.007 0.001 TRP C 92 HIS 0.003 0.001 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15620) covalent geometry : angle 0.54391 / 0.28 (21095) hydrogen bonds : bond 0.03425 / 2.31 ( 665) hydrogen bonds : angle 4.04404 / 2.79 ( 2055) link_BETA1-4 : bond 0.00551 / 0.32 ( 5) link_BETA1-4 : angle 3.10900 / 1.67 ( 15) link_NAG-ASN : bond 0.00257 / 0.15 ( 5) link_NAG-ASN : angle 4.41137 / 2.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9073 (mm) REVERT: B 121 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8265 (p0) REVERT: B 187 MET cc_start: 0.9038 (mmm) cc_final: 0.8676 (mmm) REVERT: C 80 MET cc_start: 0.9174 (mmm) cc_final: 0.8813 (mtm) REVERT: C 121 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8093 (p0) REVERT: C 134 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8175 (tp30) REVERT: D 80 MET cc_start: 0.9222 (mmm) cc_final: 0.8936 (mmt) REVERT: D 164 MET cc_start: 0.9390 (mtp) cc_final: 0.9088 (mtt) REVERT: E 134 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8412 (tp30) REVERT: E 187 MET cc_start: 0.9037 (mmm) cc_final: 0.8756 (mmm) outliers start: 39 outliers final: 32 residues processed: 134 average time/residue: 0.0896 time to fit residues: 20.0097 Evaluate side-chains 136 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063484 restraints weight = 40111.754| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.45 r_work: 0.2792 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15630 Z= 0.134 Angle : 0.572 8.229 21125 Z= 0.287 Chirality : 0.044 0.152 2355 Planarity : 0.003 0.025 2600 Dihedral : 7.755 55.037 2175 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.32 % Allowed : 18.35 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1790 helix: 1.48 (0.21), residues: 660 sheet: 0.14 (0.25), residues: 465 loop : -1.74 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 276 TYR 0.018 0.001 TYR D 325 PHE 0.011 0.001 PHE E 72 TRP 0.008 0.001 TRP C 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (15620) covalent geometry : angle 0.55377 / 0.28 (21095) hydrogen bonds : bond 0.03452 / 2.33 ( 665) hydrogen bonds : angle 4.04863 / 2.80 ( 2055) link_BETA1-4 : bond 0.00493 / 0.29 ( 5) link_BETA1-4 : angle 3.06960 / 1.63 ( 15) link_NAG-ASN : bond 0.00112 / 0.06 ( 5) link_NAG-ASN : angle 4.44062 / 2.67 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9110 (mm) REVERT: B 121 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 138 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8236 (t0) REVERT: B 187 MET cc_start: 0.9040 (mmm) cc_final: 0.8680 (mmm) REVERT: C 121 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (p0) REVERT: C 134 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8205 (tp30) REVERT: D 80 MET cc_start: 0.9208 (mmm) cc_final: 0.8927 (mmt) REVERT: D 164 MET cc_start: 0.9396 (mtp) cc_final: 0.9107 (mtt) REVERT: D 187 MET cc_start: 0.9222 (tpt) cc_final: 0.8939 (tpt) REVERT: E 134 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8356 (tp30) REVERT: E 187 MET cc_start: 0.9055 (mmm) cc_final: 0.8778 (mmm) REVERT: E 323 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9280 (mm) outliers start: 38 outliers final: 31 residues processed: 134 average time/residue: 0.0871 time to fit residues: 19.5616 Evaluate side-chains 137 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 0.3980 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.084922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.064831 restraints weight = 40296.775| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.46 r_work: 0.2821 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15630 Z= 0.104 Angle : 0.553 8.293 21125 Z= 0.277 Chirality : 0.043 0.150 2355 Planarity : 0.003 0.027 2600 Dihedral : 7.438 54.554 2175 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.02 % Allowed : 18.78 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1790 helix: 1.53 (0.21), residues: 660 sheet: 0.27 (0.25), residues: 465 loop : -1.74 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 276 TYR 0.015 0.001 TYR D 325 PHE 0.012 0.001 PHE C 319 TRP 0.010 0.001 TRP C 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (15620) covalent geometry : angle 0.53597 / 0.27 (21095) hydrogen bonds : bond 0.03230 / 2.17 ( 665) hydrogen bonds : angle 3.91822 / 2.69 ( 2055) link_BETA1-4 : bond 0.00534 / 0.31 ( 5) link_BETA1-4 : angle 3.01447 / 1.62 ( 15) link_NAG-ASN : bond 0.00282 / 0.16 ( 5) link_NAG-ASN : angle 4.11785 / 2.45 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3580 Ramachandran restraints generated. 1790 Oldfield, 0 Emsley, 1790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9136 (mm) REVERT: B 121 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8241 (p0) REVERT: B 138 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8211 (t0) REVERT: C 77 GLU cc_start: 0.7730 (pp20) cc_final: 0.7525 (pp20) REVERT: C 121 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8080 (p0) REVERT: C 134 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8141 (tp30) REVERT: C 187 MET cc_start: 0.8972 (tpp) cc_final: 0.8648 (mpp) REVERT: D 80 MET cc_start: 0.9186 (mmm) cc_final: 0.8913 (mmt) REVERT: D 164 MET cc_start: 0.9381 (mtp) cc_final: 0.9112 (mtt) REVERT: D 187 MET cc_start: 0.9207 (tpt) cc_final: 0.8699 (tpp) REVERT: E 134 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8322 (tp30) REVERT: E 187 MET cc_start: 0.9002 (mmm) cc_final: 0.8772 (mmm) REVERT: E 323 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9292 (mm) outliers start: 33 outliers final: 25 residues processed: 133 average time/residue: 0.0899 time to fit residues: 20.2372 Evaluate side-chains 136 residues out of total 1635 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 0.0980 chunk 151 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 0.0170 chunk 41 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063780 restraints weight = 40388.059| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.49 r_work: 0.2790 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15630 Z= 0.125 Angle : 0.563 8.694 21125 Z= 0.283 Chirality : 0.043 0.149 2355 Planarity : 0.003 0.026 2600 Dihedral : 7.369 54.160 2175 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.20 % Allowed : 18.65 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1790 helix: 1.58 (0.21), residues: 660 sheet: 0.31 (0.25), residues: 465 loop : -1.75 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 276 TYR 0.018 0.001 TYR D 325 PHE 0.011 0.001 PHE C 319 TRP 0.009 0.001 TRP C 92 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15620) covalent geometry : angle 0.54669 / 0.28 (21095) hydrogen bonds : bond 0.03341 / 2.25 ( 665) hydrogen bonds : angle 3.95115 / 2.72 ( 2055) link_BETA1-4 : bond 0.00489 / 0.29 ( 5) link_BETA1-4 : angle 2.95638 / 1.57 ( 15) link_NAG-ASN : bond 0.00091 / 0.05 ( 5) link_NAG-ASN : angle 4.23498 / 2.55 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.68 seconds wall clock time: 46 minutes 50.30 seconds (2810.30 seconds total)