Starting phenix.real_space_refine on Mon Apr 6 01:30:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.map" model { file = "/net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y95_72689/04_2026/9y95_72689.cif" } resolution = 3.45 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9388 2.51 5 N 2271 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14367 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2773 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2782 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2771 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2771 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 113 Unusual residues: {'NAG': 2, 'PX4': 4, 'RI5': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {'NAG': 2, 'PX4': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PX4:plan-1': 4} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.79, per 1000 atoms: 0.26 Number of scatterers: 14367 At special positions: 0 Unit cell: (94.08, 92.4, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2618 8.00 N 2271 7.00 C 9388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.03 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 NAG-ASN " NAG A 501 " - " ASN A 72 " " NAG A 502 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 502 " - " ASN E 72 " " NAG E 503 " - " ASN E 103 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 505.3 milliseconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 38.0% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.840A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.607A pdb=" N SER A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 282 through 305 Processing helix chain 'A' and resid 315 through 345 removed outlier: 3.577A pdb=" N HIS A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 443 removed outlier: 3.635A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.728A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 126 " --> pdb=" O MET B 123 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 261 through 274 removed outlier: 3.822A pdb=" N SER B 265 " --> pdb=" O MET B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 278 removed outlier: 3.533A pdb=" N ILE B 278 " --> pdb=" O SER B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 278' Processing helix chain 'B' and resid 282 through 306 removed outlier: 4.010A pdb=" N ALA B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 347 removed outlier: 3.535A pdb=" N HIS B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 443 removed outlier: 3.731A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'C' and resid 43 through 52 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.565A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 282 through 306 removed outlier: 4.043A pdb=" N ALA C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 347 removed outlier: 3.636A pdb=" N HIS C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 443 removed outlier: 3.733A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'D' and resid 43 through 52 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.774A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 262 through 275 removed outlier: 4.034A pdb=" N SER D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 282 through 305 Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 413 through 443 removed outlier: 3.616A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'E' and resid 43 through 52 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.938A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 261 through 274 removed outlier: 3.830A pdb=" N SER E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 Processing helix chain 'E' and resid 282 through 306 removed outlier: 3.929A pdb=" N ALA E 306 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 345 removed outlier: 3.531A pdb=" N HIS E 345 " --> pdb=" O VAL E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 443 removed outlier: 3.709A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.538A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.538A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.737A pdb=" N GLU A 245 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.529A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.529A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.794A pdb=" N GLU B 245 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.678A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.678A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'C' and resid 132 through 134 removed outlier: 3.517A pdb=" N GLU C 245 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'D' and resid 116 through 118 removed outlier: 4.547A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 71 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLU D 203 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL D 73 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 141 through 142 removed outlier: 5.885A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 132 through 134 Processing sheet with id=AC1, first strand: chain 'D' and resid 132 through 134 removed outlier: 3.550A pdb=" N GLU D 245 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC3, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.448A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 137 through 141 removed outlier: 6.115A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 134 removed outlier: 3.529A pdb=" N SER E 192 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR E 242 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY E 194 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N LYS E 240 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU E 245 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 221 through 223 853 hydrogen bonds defined for protein. 2487 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: 2.37 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2376 1.32 - 1.45: 3992 1.45 - 1.58: 8176 1.58 - 1.71: 2 1.71 - 1.83: 150 Bond restraints: 14696 Sorted by residual: bond pdb=" N ILE C 127 " pdb=" CA ILE C 127 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.76e+00 bond pdb=" N ASP D 175 " pdb=" CA ASP D 175 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.28e-02 6.10e+03 7.13e+00 bond pdb=" N ILE C 291 " pdb=" CA ILE C 291 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.99e+00 bond pdb=" N ILE B 291 " pdb=" CA ILE B 291 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.98e+00 bond pdb=" N ILE A 291 " pdb=" CA ILE A 291 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.85e+00 ... (remaining 14691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19430 1.75 - 3.50: 364 3.50 - 5.24: 38 5.24 - 6.99: 20 6.99 - 8.74: 6 Bond angle restraints: 19858 Sorted by residual: angle pdb=" CA GLY E 53 " pdb=" C GLY E 53 " pdb=" O GLY E 53 " ideal model delta sigma weight residual 120.91 118.21 2.70 6.90e-01 2.10e+00 1.53e+01 angle pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" O GLY B 53 " ideal model delta sigma weight residual 120.91 118.34 2.57 6.90e-01 2.10e+00 1.39e+01 angle pdb=" CA CYS D 232 " pdb=" CB CYS D 232 " pdb=" SG CYS D 232 " ideal model delta sigma weight residual 114.40 121.88 -7.48 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CA CYS A 232 " pdb=" CB CYS A 232 " pdb=" SG CYS A 232 " ideal model delta sigma weight residual 114.40 121.73 -7.33 2.30e+00 1.89e-01 1.01e+01 angle pdb=" N THR C 292 " pdb=" CA THR C 292 " pdb=" C THR C 292 " ideal model delta sigma weight residual 111.36 107.96 3.40 1.09e+00 8.42e-01 9.74e+00 ... (remaining 19853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8089 17.62 - 35.25: 705 35.25 - 52.87: 166 52.87 - 70.49: 38 70.49 - 88.12: 5 Dihedral angle restraints: 9003 sinusoidal: 3924 harmonic: 5079 Sorted by residual: dihedral pdb=" CB CYS A 232 " pdb=" SG CYS A 232 " pdb=" SG CYS A 243 " pdb=" CB CYS A 243 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS D 232 " pdb=" SG CYS D 232 " pdb=" SG CYS D 243 " pdb=" CB CYS D 243 " ideal model delta sinusoidal sigma weight residual 93.00 55.34 37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA ILE E 96 " pdb=" C ILE E 96 " pdb=" N PHE E 97 " pdb=" CA PHE E 97 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1958 0.066 - 0.133: 263 0.133 - 0.199: 20 0.199 - 0.266: 1 0.266 - 0.332: 1 Chirality restraints: 2243 Sorted by residual: chirality pdb=" C06 RI5 A 506 " pdb=" C05 RI5 A 506 " pdb=" C07 RI5 A 506 " pdb=" O19 RI5 A 506 " both_signs ideal model delta sigma weight residual False 2.58 2.91 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C08 RI5 A 506 " pdb=" C07 RI5 A 506 " pdb=" C09 RI5 A 506 " pdb=" C13 RI5 A 506 " both_signs ideal model delta sigma weight residual False 2.99 2.73 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 2240 not shown) Planarity restraints: 2458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 72 " -0.018 2.00e-02 2.50e+03 1.70e-02 3.61e+00 pdb=" CG ASN E 72 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 72 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 72 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG E 502 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 72 " 0.018 2.00e-02 2.50e+03 1.69e-02 3.55e+00 pdb=" CG ASN B 72 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 72 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 72 " -0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 72 " -0.018 2.00e-02 2.50e+03 1.68e-02 3.54e+00 pdb=" CG ASN D 72 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN D 72 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 72 " 0.016 2.00e-02 2.50e+03 pdb=" C1 NAG D 501 " -0.017 2.00e-02 2.50e+03 ... (remaining 2455 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2193 2.76 - 3.30: 13066 3.30 - 3.83: 22899 3.83 - 4.37: 26865 4.37 - 4.90: 48080 Nonbonded interactions: 113103 Sorted by model distance: nonbonded pdb=" OG1 THR D 196 " pdb=" OD1 ASN D 198 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR B 196 " pdb=" OD1 ASN B 198 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR C 196 " pdb=" OD1 ASN C 198 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR E 196 " pdb=" OD1 ASN E 198 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 196 " pdb=" OD1 ASN A 198 " model vdw 2.261 3.040 ... (remaining 113098 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 41 through 345 or resid 413 through 449 or resid 502 or re \ sid 504 through 505)) selection = (chain 'B' and (resid 41 through 345 or resid 413 through 449 or resid 502 or re \ sid 504 through 505)) selection = (chain 'C' and (resid 41 through 345 or resid 413 through 449 or resid 502 or re \ sid 504 through 505)) selection = (chain 'D' and (resid 41 through 345 or resid 413 through 449 or resid 502 or re \ sid 504 through 505)) selection = (chain 'E' and (resid 41 through 345 or resid 413 through 449 or resid 502 or re \ sid 504 through 505)) } 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14716 Z= 0.184 Angle : 0.618 10.166 19908 Z= 0.336 Chirality : 0.046 0.332 2243 Planarity : 0.004 0.044 2448 Dihedral : 13.927 88.116 5677 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.15 (0.20), residues: 1698 helix: 0.66 (0.21), residues: 564 sheet: -0.15 (0.28), residues: 408 loop : -0.55 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 305 TYR 0.016 0.001 TYR B 335 PHE 0.018 0.001 PHE B 97 TRP 0.010 0.001 TRP D 204 HIS 0.004 0.000 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00323 (14696) covalent geometry : angle 0.59268 (19858) SS BOND : bond 0.00156 ( 10) SS BOND : angle 2.41946 ( 20) hydrogen bonds : bond 0.20885 ( 697) hydrogen bonds : angle 7.92901 ( 2487) link_NAG-ASN : bond 0.00353 ( 10) link_NAG-ASN : angle 4.13230 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.471 Fit side-chains REVERT: A 87 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 175 ASP cc_start: 0.8147 (t0) cc_final: 0.7847 (t0) REVERT: A 197 MET cc_start: 0.9179 (tpt) cc_final: 0.8483 (tpp) REVERT: A 259 ILE cc_start: 0.9358 (tp) cc_final: 0.9148 (tp) REVERT: A 304 SER cc_start: 0.9433 (m) cc_final: 0.9180 (p) REVERT: B 112 TYR cc_start: 0.7424 (t80) cc_final: 0.7184 (t80) REVERT: B 197 MET cc_start: 0.9045 (tpp) cc_final: 0.8373 (tpp) REVERT: B 240 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8661 (mtmm) REVERT: C 220 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8686 (mm-40) REVERT: C 259 ILE cc_start: 0.9370 (tp) cc_final: 0.9078 (tp) REVERT: C 260 GLN cc_start: 0.8930 (mm110) cc_final: 0.8239 (mm110) REVERT: C 279 ASN cc_start: 0.8253 (t0) cc_final: 0.7787 (t0) REVERT: C 304 SER cc_start: 0.9538 (m) cc_final: 0.9296 (m) REVERT: C 422 SER cc_start: 0.9392 (m) cc_final: 0.9065 (p) REVERT: D 191 GLU cc_start: 0.8676 (tt0) cc_final: 0.8298 (tt0) REVERT: D 334 GLU cc_start: 0.9285 (tm-30) cc_final: 0.8622 (tm-30) REVERT: D 344 GLN cc_start: 0.8486 (pp30) cc_final: 0.8269 (pp30) REVERT: D 414 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7794 (ttp80) REVERT: E 52 MET cc_start: 0.7340 (ttp) cc_final: 0.6913 (ppp) REVERT: E 61 ARG cc_start: 0.9000 (mtm-85) cc_final: 0.8579 (mpp80) REVERT: E 131 ASP cc_start: 0.9184 (p0) cc_final: 0.8570 (p0) REVERT: E 188 MET cc_start: 0.9177 (ttm) cc_final: 0.8917 (ttm) REVERT: E 203 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8047 (mm-30) REVERT: E 211 GLN cc_start: 0.8712 (mt0) cc_final: 0.8387 (mt0) REVERT: E 225 GLU cc_start: 0.8822 (tp30) cc_final: 0.8491 (tm-30) REVERT: E 228 GLU cc_start: 0.7804 (mp0) cc_final: 0.7517 (mp0) REVERT: E 251 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8069 (mt-10) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1291 time to fit residues: 48.1602 Evaluate side-chains 177 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 300 GLN A 344 GLN B 300 GLN B 344 GLN C 300 GLN E 345 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080767 restraints weight = 25921.577| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.00 r_work: 0.2853 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14716 Z= 0.133 Angle : 0.572 9.168 19908 Z= 0.298 Chirality : 0.043 0.143 2243 Planarity : 0.004 0.066 2448 Dihedral : 8.485 59.411 2376 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.97 % Allowed : 7.30 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.63 (0.20), residues: 1698 helix: 1.87 (0.21), residues: 577 sheet: 0.16 (0.27), residues: 402 loop : -0.59 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 343 TYR 0.022 0.001 TYR B 335 PHE 0.015 0.001 PHE B 97 TRP 0.010 0.001 TRP C 102 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00279 (14696) covalent geometry : angle 0.56006 (19858) SS BOND : bond 0.00871 ( 10) SS BOND : angle 1.68100 ( 20) hydrogen bonds : bond 0.05660 ( 697) hydrogen bonds : angle 5.08796 ( 2487) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 2.68845 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.555 Fit side-chains REVERT: A 87 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 175 ASP cc_start: 0.8152 (t0) cc_final: 0.7885 (t0) REVERT: A 197 MET cc_start: 0.9052 (tpt) cc_final: 0.8539 (tpp) REVERT: A 300 GLN cc_start: 0.9250 (tp-100) cc_final: 0.9023 (tp-100) REVERT: C 220 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8881 (mm-40) REVERT: C 279 ASN cc_start: 0.8368 (t0) cc_final: 0.7978 (t0) REVERT: C 300 GLN cc_start: 0.9609 (tp-100) cc_final: 0.9272 (tp40) REVERT: C 304 SER cc_start: 0.9272 (m) cc_final: 0.9027 (m) REVERT: D 52 MET cc_start: 0.8459 (tmm) cc_final: 0.8211 (ppp) REVERT: D 91 ASP cc_start: 0.8817 (p0) cc_final: 0.8561 (p0) REVERT: D 300 GLN cc_start: 0.9572 (tp40) cc_final: 0.9074 (tp-100) REVERT: D 305 ARG cc_start: 0.8782 (ttp-110) cc_final: 0.8555 (ttm-80) REVERT: D 334 GLU cc_start: 0.9332 (tm-30) cc_final: 0.8649 (tm-30) REVERT: E 52 MET cc_start: 0.7697 (ttp) cc_final: 0.7411 (ppp) outliers start: 15 outliers final: 8 residues processed: 207 average time/residue: 0.1120 time to fit residues: 34.4159 Evaluate side-chains 179 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 184 GLN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080654 restraints weight = 26331.952| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.98 r_work: 0.2846 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14716 Z= 0.130 Angle : 0.557 8.356 19908 Z= 0.287 Chirality : 0.043 0.212 2243 Planarity : 0.004 0.053 2448 Dihedral : 8.202 59.498 2376 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.10 % Allowed : 9.95 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.91 (0.21), residues: 1698 helix: 2.28 (0.21), residues: 571 sheet: 0.32 (0.27), residues: 404 loop : -0.58 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.022 0.001 TYR B 335 PHE 0.014 0.001 PHE E 97 TRP 0.011 0.001 TRP C 102 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00289 (14696) covalent geometry : angle 0.54592 (19858) SS BOND : bond 0.00464 ( 10) SS BOND : angle 1.94204 ( 20) hydrogen bonds : bond 0.04666 ( 697) hydrogen bonds : angle 4.60162 ( 2487) link_NAG-ASN : bond 0.00244 ( 10) link_NAG-ASN : angle 2.40562 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 175 ASP cc_start: 0.8138 (t0) cc_final: 0.7884 (t0) REVERT: A 197 MET cc_start: 0.8951 (tpt) cc_final: 0.8438 (tpp) REVERT: A 300 GLN cc_start: 0.9264 (tp-100) cc_final: 0.8757 (tp-100) REVERT: B 345 HIS cc_start: 0.7511 (m-70) cc_final: 0.6457 (t70) REVERT: C 279 ASN cc_start: 0.8273 (t0) cc_final: 0.7904 (t0) REVERT: C 304 SER cc_start: 0.9251 (m) cc_final: 0.9012 (m) REVERT: D 300 GLN cc_start: 0.9581 (tp40) cc_final: 0.9114 (tp-100) REVERT: D 305 ARG cc_start: 0.8808 (ttp-110) cc_final: 0.8563 (ttm-80) REVERT: D 334 GLU cc_start: 0.9390 (tm-30) cc_final: 0.8713 (tm-30) REVERT: E 52 MET cc_start: 0.7730 (ttp) cc_final: 0.7468 (ppp) outliers start: 17 outliers final: 12 residues processed: 200 average time/residue: 0.1225 time to fit residues: 35.9065 Evaluate side-chains 180 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081336 restraints weight = 26071.772| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.04 r_work: 0.2853 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14716 Z= 0.124 Angle : 0.542 10.244 19908 Z= 0.279 Chirality : 0.042 0.162 2243 Planarity : 0.003 0.040 2448 Dihedral : 8.055 59.971 2376 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 12.08 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.02 (0.21), residues: 1698 helix: 2.35 (0.21), residues: 572 sheet: 0.38 (0.27), residues: 408 loop : -0.50 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 54 TYR 0.021 0.001 TYR D 335 PHE 0.014 0.001 PHE E 329 TRP 0.009 0.001 TRP C 102 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00274 (14696) covalent geometry : angle 0.53278 (19858) SS BOND : bond 0.00569 ( 10) SS BOND : angle 1.57978 ( 20) hydrogen bonds : bond 0.04271 ( 697) hydrogen bonds : angle 4.35211 ( 2487) link_NAG-ASN : bond 0.00240 ( 10) link_NAG-ASN : angle 2.27192 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 175 ASP cc_start: 0.8197 (t0) cc_final: 0.7917 (t0) REVERT: A 197 MET cc_start: 0.8930 (tpt) cc_final: 0.8402 (tpp) REVERT: A 300 GLN cc_start: 0.9290 (tp-100) cc_final: 0.8761 (tp-100) REVERT: B 343 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7167 (ttm110) REVERT: B 345 HIS cc_start: 0.7246 (m-70) cc_final: 0.6359 (t70) REVERT: C 279 ASN cc_start: 0.8283 (t0) cc_final: 0.7908 (t0) REVERT: C 300 GLN cc_start: 0.9632 (tp-100) cc_final: 0.9300 (tp40) REVERT: C 304 SER cc_start: 0.9306 (m) cc_final: 0.9082 (m) REVERT: D 281 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8638 (p0) REVERT: D 300 GLN cc_start: 0.9591 (tp40) cc_final: 0.9144 (tp-100) REVERT: D 305 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8574 (ttm-80) REVERT: D 334 GLU cc_start: 0.9378 (tm-30) cc_final: 0.8762 (tm-30) REVERT: E 52 MET cc_start: 0.7781 (ttp) cc_final: 0.7466 (ppp) outliers start: 18 outliers final: 14 residues processed: 193 average time/residue: 0.1236 time to fit residues: 34.9361 Evaluate side-chains 181 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 157 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.079708 restraints weight = 26325.120| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.04 r_work: 0.2822 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14716 Z= 0.175 Angle : 0.570 10.036 19908 Z= 0.293 Chirality : 0.043 0.202 2243 Planarity : 0.003 0.036 2448 Dihedral : 8.111 59.223 2376 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.74 % Allowed : 12.92 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.02 (0.21), residues: 1698 helix: 2.37 (0.21), residues: 575 sheet: 0.38 (0.27), residues: 408 loop : -0.53 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 54 TYR 0.022 0.001 TYR B 335 PHE 0.013 0.001 PHE B 329 TRP 0.010 0.001 TRP C 102 HIS 0.006 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00406 (14696) covalent geometry : angle 0.55669 (19858) SS BOND : bond 0.00319 ( 10) SS BOND : angle 2.69050 ( 20) hydrogen bonds : bond 0.04367 ( 697) hydrogen bonds : angle 4.30142 ( 2487) link_NAG-ASN : bond 0.00314 ( 10) link_NAG-ASN : angle 2.33993 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 175 ASP cc_start: 0.8175 (t0) cc_final: 0.7895 (t0) REVERT: A 197 MET cc_start: 0.8940 (tpt) cc_final: 0.8354 (tpp) REVERT: A 300 GLN cc_start: 0.9360 (tp-100) cc_final: 0.8835 (tp-100) REVERT: B 343 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7068 (ttm110) REVERT: B 345 HIS cc_start: 0.7199 (m-70) cc_final: 0.6151 (t70) REVERT: C 279 ASN cc_start: 0.8272 (t0) cc_final: 0.7898 (t0) REVERT: D 300 GLN cc_start: 0.9589 (tp40) cc_final: 0.9136 (tp-100) REVERT: D 334 GLU cc_start: 0.9393 (tm-30) cc_final: 0.8805 (tm-30) REVERT: E 52 MET cc_start: 0.7905 (ttp) cc_final: 0.7464 (ppp) outliers start: 27 outliers final: 18 residues processed: 189 average time/residue: 0.1227 time to fit residues: 34.0886 Evaluate side-chains 182 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 304 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 345 HIS ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082167 restraints weight = 26090.792| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.04 r_work: 0.2868 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14716 Z= 0.105 Angle : 0.538 9.770 19908 Z= 0.276 Chirality : 0.042 0.141 2243 Planarity : 0.003 0.040 2448 Dihedral : 7.856 58.245 2376 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.00 % Allowed : 13.70 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.15 (0.21), residues: 1698 helix: 2.47 (0.21), residues: 573 sheet: 0.48 (0.27), residues: 408 loop : -0.45 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 54 TYR 0.019 0.001 TYR D 335 PHE 0.013 0.001 PHE E 329 TRP 0.008 0.001 TRP C 102 HIS 0.016 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00224 (14696) covalent geometry : angle 0.52710 (19858) SS BOND : bond 0.00524 ( 10) SS BOND : angle 2.31333 ( 20) hydrogen bonds : bond 0.03920 ( 697) hydrogen bonds : angle 4.09657 ( 2487) link_NAG-ASN : bond 0.00264 ( 10) link_NAG-ASN : angle 2.14132 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8175 (t0) cc_final: 0.7888 (t0) REVERT: A 197 MET cc_start: 0.8901 (tpt) cc_final: 0.8311 (tpp) REVERT: A 300 GLN cc_start: 0.9306 (tp-100) cc_final: 0.8772 (tp-100) REVERT: B 254 MET cc_start: 0.8451 (ttp) cc_final: 0.8168 (tmm) REVERT: B 343 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7046 (ttm110) REVERT: C 254 MET cc_start: 0.8680 (mmm) cc_final: 0.8293 (mmm) REVERT: C 279 ASN cc_start: 0.8243 (t0) cc_final: 0.7842 (t0) REVERT: D 300 GLN cc_start: 0.9576 (tp40) cc_final: 0.9146 (tp-100) REVERT: D 305 ARG cc_start: 0.8925 (ttp-110) cc_final: 0.8610 (mtm-85) REVERT: D 334 GLU cc_start: 0.9385 (tm-30) cc_final: 0.8843 (tm-30) REVERT: E 52 MET cc_start: 0.7772 (ttp) cc_final: 0.7459 (ppp) outliers start: 31 outliers final: 25 residues processed: 210 average time/residue: 0.1196 time to fit residues: 37.0380 Evaluate side-chains 192 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 310 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 260 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.099968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080625 restraints weight = 26323.348| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.05 r_work: 0.2841 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14716 Z= 0.148 Angle : 0.558 8.662 19908 Z= 0.286 Chirality : 0.043 0.177 2243 Planarity : 0.003 0.044 2448 Dihedral : 7.895 57.763 2376 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.13 % Allowed : 14.28 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1698 helix: 2.41 (0.21), residues: 575 sheet: 0.52 (0.27), residues: 408 loop : -0.45 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 54 TYR 0.021 0.001 TYR D 335 PHE 0.012 0.001 PHE B 133 TRP 0.009 0.001 TRP C 102 HIS 0.006 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00342 (14696) covalent geometry : angle 0.54565 (19858) SS BOND : bond 0.00530 ( 10) SS BOND : angle 2.48010 ( 20) hydrogen bonds : bond 0.04031 ( 697) hydrogen bonds : angle 4.13107 ( 2487) link_NAG-ASN : bond 0.00283 ( 10) link_NAG-ASN : angle 2.26324 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8220 (t0) cc_final: 0.7930 (t0) REVERT: A 197 MET cc_start: 0.8898 (tpt) cc_final: 0.8301 (tpp) REVERT: A 232 CYS cc_start: 0.5489 (t) cc_final: 0.5212 (t) REVERT: A 300 GLN cc_start: 0.9374 (tp-100) cc_final: 0.8812 (tp-100) REVERT: B 254 MET cc_start: 0.8442 (ttp) cc_final: 0.8224 (tmm) REVERT: B 343 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6961 (ttm110) REVERT: C 254 MET cc_start: 0.8699 (mmm) cc_final: 0.8342 (mmm) REVERT: C 279 ASN cc_start: 0.8262 (t0) cc_final: 0.7853 (t0) REVERT: D 300 GLN cc_start: 0.9596 (tp40) cc_final: 0.9148 (tp-100) REVERT: D 305 ARG cc_start: 0.8924 (ttp-110) cc_final: 0.8618 (mtm-85) REVERT: D 334 GLU cc_start: 0.9411 (tm-30) cc_final: 0.8855 (tm-30) REVERT: E 52 MET cc_start: 0.7878 (ttp) cc_final: 0.7439 (ppp) outliers start: 33 outliers final: 27 residues processed: 191 average time/residue: 0.1157 time to fit residues: 32.7715 Evaluate side-chains 198 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 343 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 310 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.100928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081616 restraints weight = 26093.922| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.05 r_work: 0.2858 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14716 Z= 0.123 Angle : 0.572 11.663 19908 Z= 0.291 Chirality : 0.043 0.254 2243 Planarity : 0.003 0.074 2448 Dihedral : 7.869 57.781 2376 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.13 % Allowed : 14.66 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.20 (0.21), residues: 1698 helix: 2.47 (0.21), residues: 574 sheet: 0.55 (0.27), residues: 408 loop : -0.43 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 54 TYR 0.019 0.001 TYR E 335 PHE 0.013 0.001 PHE B 133 TRP 0.008 0.001 TRP C 102 HIS 0.005 0.000 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00276 (14696) covalent geometry : angle 0.55567 (19858) SS BOND : bond 0.00421 ( 10) SS BOND : angle 3.04814 ( 20) hydrogen bonds : bond 0.03975 ( 697) hydrogen bonds : angle 4.07732 ( 2487) link_NAG-ASN : bond 0.00343 ( 10) link_NAG-ASN : angle 2.50561 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8191 (t0) cc_final: 0.7902 (t0) REVERT: A 197 MET cc_start: 0.8830 (tpt) cc_final: 0.8237 (tpp) REVERT: A 232 CYS cc_start: 0.5452 (t) cc_final: 0.5190 (t) REVERT: A 300 GLN cc_start: 0.9364 (tp-100) cc_final: 0.8785 (tp-100) REVERT: C 254 MET cc_start: 0.8674 (mmm) cc_final: 0.8391 (mmm) REVERT: C 279 ASN cc_start: 0.8261 (t0) cc_final: 0.7860 (t0) REVERT: C 300 GLN cc_start: 0.9639 (tp40) cc_final: 0.9428 (tm-30) REVERT: D 300 GLN cc_start: 0.9581 (tp40) cc_final: 0.9144 (tp-100) REVERT: D 305 ARG cc_start: 0.8925 (ttp-110) cc_final: 0.8626 (mtm-85) REVERT: D 334 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9154 (tm-30) REVERT: E 52 MET cc_start: 0.7881 (ttp) cc_final: 0.7475 (ppp) outliers start: 33 outliers final: 27 residues processed: 199 average time/residue: 0.1181 time to fit residues: 34.8983 Evaluate side-chains 195 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 310 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 159 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080244 restraints weight = 26406.516| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.05 r_work: 0.2833 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14716 Z= 0.166 Angle : 0.596 10.149 19908 Z= 0.304 Chirality : 0.043 0.197 2243 Planarity : 0.003 0.045 2448 Dihedral : 7.962 57.672 2376 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.13 % Allowed : 14.41 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.15 (0.21), residues: 1698 helix: 2.44 (0.21), residues: 575 sheet: 0.45 (0.27), residues: 418 loop : -0.42 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 54 TYR 0.021 0.001 TYR D 335 PHE 0.014 0.001 PHE E 329 TRP 0.009 0.001 TRP C 102 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00386 (14696) covalent geometry : angle 0.57894 (19858) SS BOND : bond 0.00379 ( 10) SS BOND : angle 3.26133 ( 20) hydrogen bonds : bond 0.04113 ( 697) hydrogen bonds : angle 4.16801 ( 2487) link_NAG-ASN : bond 0.00324 ( 10) link_NAG-ASN : angle 2.56044 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8185 (t0) cc_final: 0.7905 (t0) REVERT: A 197 MET cc_start: 0.8845 (tpt) cc_final: 0.8239 (tpp) REVERT: A 232 CYS cc_start: 0.5526 (t) cc_final: 0.5261 (t) REVERT: A 300 GLN cc_start: 0.9385 (tp-100) cc_final: 0.8818 (tp-100) REVERT: C 254 MET cc_start: 0.8677 (mmm) cc_final: 0.8409 (mmm) REVERT: C 279 ASN cc_start: 0.8280 (t0) cc_final: 0.7879 (t0) REVERT: D 61 ARG cc_start: 0.9074 (mtm-85) cc_final: 0.8692 (mtp85) REVERT: D 172 CYS cc_start: 0.7304 (t) cc_final: 0.7072 (t) REVERT: D 300 GLN cc_start: 0.9587 (tp40) cc_final: 0.9123 (tp-100) REVERT: D 305 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8657 (mtm-85) REVERT: D 334 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9156 (tm-30) REVERT: E 52 MET cc_start: 0.7935 (ttp) cc_final: 0.7376 (ppp) outliers start: 33 outliers final: 31 residues processed: 191 average time/residue: 0.1168 time to fit residues: 33.2141 Evaluate side-chains 198 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain E residue 310 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 104 optimal weight: 0.0470 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082667 restraints weight = 25953.479| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.04 r_work: 0.2880 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14716 Z= 0.107 Angle : 0.569 10.276 19908 Z= 0.289 Chirality : 0.042 0.171 2243 Planarity : 0.004 0.061 2448 Dihedral : 7.760 58.318 2376 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.87 % Allowed : 14.92 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.24 (0.21), residues: 1698 helix: 2.48 (0.21), residues: 575 sheet: 0.50 (0.27), residues: 418 loop : -0.35 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 54 TYR 0.019 0.001 TYR D 335 PHE 0.014 0.001 PHE D 329 TRP 0.008 0.001 TRP C 102 HIS 0.005 0.000 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00231 (14696) covalent geometry : angle 0.55456 (19858) SS BOND : bond 0.00263 ( 10) SS BOND : angle 2.88500 ( 20) hydrogen bonds : bond 0.03831 ( 697) hydrogen bonds : angle 4.02335 ( 2487) link_NAG-ASN : bond 0.00279 ( 10) link_NAG-ASN : angle 2.31510 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8170 (t0) cc_final: 0.7896 (t0) REVERT: A 197 MET cc_start: 0.8798 (tpt) cc_final: 0.8213 (tpp) REVERT: A 232 CYS cc_start: 0.5323 (t) cc_final: 0.5057 (t) REVERT: A 300 GLN cc_start: 0.9348 (tp-100) cc_final: 0.8775 (tp-100) REVERT: C 123 MET cc_start: 0.8318 (mtm) cc_final: 0.8081 (ptp) REVERT: C 254 MET cc_start: 0.8605 (mmm) cc_final: 0.8344 (mmm) REVERT: C 279 ASN cc_start: 0.8256 (t0) cc_final: 0.7868 (t0) REVERT: D 61 ARG cc_start: 0.9058 (mtm-85) cc_final: 0.8747 (mtp85) REVERT: D 172 CYS cc_start: 0.7198 (t) cc_final: 0.6958 (t) REVERT: D 300 GLN cc_start: 0.9571 (tp40) cc_final: 0.9123 (tp-100) REVERT: D 305 ARG cc_start: 0.8919 (ttp-110) cc_final: 0.8690 (ttm-80) REVERT: D 334 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9156 (tm-30) REVERT: E 52 MET cc_start: 0.7894 (ttp) cc_final: 0.7432 (ppp) outliers start: 29 outliers final: 27 residues processed: 205 average time/residue: 0.1138 time to fit residues: 34.8874 Evaluate side-chains 203 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 302 SER Chi-restraints excluded: chain E residue 310 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 130 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN D 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080572 restraints weight = 26407.803| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.06 r_work: 0.2841 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14716 Z= 0.164 Angle : 0.593 10.210 19908 Z= 0.303 Chirality : 0.043 0.159 2243 Planarity : 0.004 0.080 2448 Dihedral : 7.853 59.526 2376 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.87 % Allowed : 15.18 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.18 (0.21), residues: 1698 helix: 2.47 (0.21), residues: 575 sheet: 0.44 (0.27), residues: 418 loop : -0.40 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 54 TYR 0.021 0.001 TYR D 335 PHE 0.021 0.001 PHE D 329 TRP 0.009 0.001 TRP C 102 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00381 (14696) covalent geometry : angle 0.57893 (19858) SS BOND : bond 0.00268 ( 10) SS BOND : angle 2.88484 ( 20) hydrogen bonds : bond 0.04036 ( 697) hydrogen bonds : angle 4.12912 ( 2487) link_NAG-ASN : bond 0.00327 ( 10) link_NAG-ASN : angle 2.48579 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.34 seconds wall clock time: 41 minutes 23.26 seconds (2483.26 seconds total)