Starting phenix.real_space_refine on Sat Sep 12 14:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uzy_20964/09_2026/6uzy_20964.cif" } resolution = 3.38 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 77 5.16 5 C 10948 2.51 5 N 2443 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16212 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "D" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "E" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "F" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "G" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2260 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'6OU': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.56, per 1000 atoms: 0.22 Number of scatterers: 16212 At special positions: 0 Unit cell: (107.8, 107.8, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 7 15.00 O 2737 8.00 N 2443 7.00 C 10948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " 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 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 766.9 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3794 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 71.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.612A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.894A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.612A pdb=" N LEU B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.896A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 240 removed outlier: 4.098A pdb=" N LYS C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.612A pdb=" N LEU C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 286 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.611A pdb=" N LEU D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.655A pdb=" N LYS E 205 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 240 removed outlier: 4.098A pdb=" N LYS E 214 " --> pdb=" O GLY E 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 237 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 removed outlier: 3.590A pdb=" N ARG E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR E 286 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.612A pdb=" N LEU E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 339 removed outlier: 4.059A pdb=" N LEU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS F 205 " --> pdb=" O TYR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS F 214 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN F 282 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR F 286 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Proline residue: F 291 - end of helix removed outlier: 3.611A pdb=" N LEU F 298 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.613A pdb=" N TYR F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 357 removed outlier: 4.236A pdb=" N PHE F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 132 through 158 removed outlier: 3.895A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 205 removed outlier: 3.656A pdb=" N LYS G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 240 removed outlier: 4.099A pdb=" N LYS G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 237 " --> pdb=" O LEU G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 removed outlier: 3.591A pdb=" N ARG G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 286 " --> pdb=" O ASN G 282 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET G 290 " --> pdb=" O TYR G 286 " (cutoff:3.500A) Proline residue: G 291 - end of helix removed outlier: 3.612A pdb=" N LEU G 298 " --> pdb=" O ILE G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 312 removed outlier: 3.612A pdb=" N TYR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 339 removed outlier: 4.060A pdb=" N LEU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 357 removed outlier: 4.237A pdb=" N PHE G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 966 hydrogen bonds defined for protein. 2856 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: 2.75 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4238 1.34 - 1.46: 3216 1.46 - 1.58: 8863 1.58 - 1.70: 140 1.70 - 1.82: 112 Bond restraints: 16569 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU D 501 " pdb=" O18 6OU D 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU E 501 " pdb=" O18 6OU E 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 16564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 21997 3.23 - 6.46: 319 6.46 - 9.69: 70 9.69 - 12.92: 0 12.92 - 16.15: 7 Bond angle restraints: 22393 Sorted by residual: angle pdb=" N HIS F 106 " pdb=" CA HIS F 106 " pdb=" C HIS F 106 " ideal model delta sigma weight residual 111.28 118.19 -6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" N HIS D 106 " pdb=" CA HIS D 106 " pdb=" C HIS D 106 " ideal model delta sigma weight residual 111.28 118.17 -6.89 1.09e+00 8.42e-01 4.00e+01 angle pdb=" N HIS B 106 " pdb=" CA HIS B 106 " pdb=" C HIS B 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS A 106 " pdb=" CA HIS A 106 " pdb=" C HIS A 106 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" N HIS E 106 " pdb=" CA HIS E 106 " pdb=" C HIS E 106 " ideal model delta sigma weight residual 111.28 118.11 -6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 22388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 8604 16.91 - 33.82: 977 33.82 - 50.73: 261 50.73 - 67.63: 42 67.63 - 84.54: 14 Dihedral angle restraints: 9898 sinusoidal: 4067 harmonic: 5831 Sorted by residual: dihedral pdb=" C ASN B 306 " pdb=" N ASN B 306 " pdb=" CA ASN B 306 " pdb=" CB ASN B 306 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C ASN F 306 " pdb=" N ASN F 306 " pdb=" CA ASN F 306 " pdb=" CB ASN F 306 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C ASN G 306 " pdb=" N ASN G 306 " pdb=" CA ASN G 306 " pdb=" CB ASN G 306 " ideal model delta harmonic sigma weight residual -122.60 -136.42 13.82 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2457 0.112 - 0.225: 169 0.225 - 0.337: 6 0.337 - 0.450: 0 0.450 - 0.562: 14 Chirality restraints: 2646 Sorted by residual: chirality pdb=" C20 6OU G1002 " pdb=" C19 6OU G1002 " pdb=" C21 6OU G1002 " pdb=" O30 6OU G1002 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C20 6OU C 501 " pdb=" C19 6OU C 501 " pdb=" C21 6OU C 501 " pdb=" O30 6OU C 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" C20 6OU F 501 " pdb=" C19 6OU F 501 " pdb=" C21 6OU F 501 " pdb=" O30 6OU F 501 " both_signs ideal model delta sigma weight residual False 2.35 2.91 -0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 2643 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 290 " -0.032 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 291 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 291 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 291 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 290 " 0.032 5.00e-02 4.00e+02 4.73e-02 3.57e+00 pdb=" N PRO E 291 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 291 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 291 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.032 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO E 133 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.027 5.00e-02 4.00e+02 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3924 2.79 - 3.32: 14483 3.32 - 3.85: 24815 3.85 - 4.37: 29118 4.37 - 4.90: 52268 Nonbonded interactions: 124608 Sorted by model distance: nonbonded pdb=" NH2 ARG B 75 " pdb=" OD2 ASP C 81 " model vdw 2.265 3.120 nonbonded pdb=" NE2 GLN C 76 " pdb=" O ALA D 68 " model vdw 2.345 3.120 nonbonded pdb=" OH TYR G 311 " pdb=" OG SER G 346 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR F 311 " pdb=" OG SER F 346 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR B 311 " pdb=" OG SER B 346 " model vdw 2.361 3.040 ... (remaining 124603 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'B' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'C' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'D' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'E' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'F' and (resid 25 through 358 or (resid 503 and (name C28 or name C29 or \ name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37)))) selection = (chain 'G' and (resid 25 through 358 or resid 1003)) } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.850 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.012 0.136 16583 Z= 0.594 Angle : 1.097 16.145 22421 Z= 0.617 Chirality : 0.073 0.562 2646 Planarity : 0.006 0.047 2625 Dihedral : 15.174 84.542 6062 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.16), residues: 1890 helix: -1.77 (0.12), residues: 1407 sheet: -0.71 (0.54), residues: 77 loop : -3.77 (0.23), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 29 TYR 0.010 0.001 TYR G 280 PHE 0.013 0.001 PHE G 246 TRP 0.021 0.003 TRP D 74 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd/Z covalent geometry : bond 0.01168 / 0.59 (16569) covalent geometry : angle 1.09667 / 0.62 (22393) SS BOND : bond 0.00360 / 0.18 ( 14) SS BOND : angle 1.18104 / 0.71 ( 28) hydrogen bonds : bond 0.13525 / 9.03 ( 966) hydrogen bonds : angle 5.70692 / 4.00 ( 2856) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.609 Fit side-chains REVERT: B 52 LEU cc_start: 0.7830 (mt) cc_final: 0.7546 (mt) REVERT: B 128 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8006 (ttp80) REVERT: D 235 TYR cc_start: 0.7277 (t80) cc_final: 0.7036 (t80) REVERT: D 282 ASN cc_start: 0.8530 (t0) cc_final: 0.8330 (t0) REVERT: E 297 MET cc_start: 0.8656 (mtp) cc_final: 0.8428 (mtm) REVERT: F 52 LEU cc_start: 0.8004 (mt) cc_final: 0.7770 (mt) REVERT: F 235 TYR cc_start: 0.7253 (t80) cc_final: 0.7046 (t80) REVERT: G 290 MET cc_start: 0.7909 (mtp) cc_final: 0.7589 (mtt) REVERT: G 309 LYS cc_start: 0.7944 (mtpp) cc_final: 0.7704 (mtpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1429 time to fit residues: 31.7934 Evaluate side-chains 116 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 GLN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.144584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110869 restraints weight = 16516.532| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.74 r_work: 0.3022 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16583 Z= 0.104 Angle : 0.513 5.865 22421 Z= 0.259 Chirality : 0.037 0.123 2646 Planarity : 0.004 0.030 2625 Dihedral : 7.435 55.702 2359 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.34 % Allowed : 11.17 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1890 helix: 0.33 (0.14), residues: 1435 sheet: -2.98 (0.54), residues: 84 loop : -2.75 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.006 0.001 TYR E 215 PHE 0.005 0.001 PHE C 109 TRP 0.010 0.001 TRP D 74 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (16569) covalent geometry : angle 0.51164 / 0.26 (22393) SS BOND : bond 0.00135 / 0.08 ( 14) SS BOND : angle 1.22294 / 0.72 ( 28) hydrogen bonds : bond 0.03747 / 2.48 ( 966) hydrogen bonds : angle 3.63152 / 2.58 ( 2856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.601 Fit side-chains REVERT: A 203 LYS cc_start: 0.8258 (mmmm) cc_final: 0.8033 (mtpt) REVERT: B 52 LEU cc_start: 0.7616 (mt) cc_final: 0.7374 (mt) REVERT: B 128 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8573 (ttp80) REVERT: B 290 MET cc_start: 0.7783 (mtp) cc_final: 0.7536 (mtt) REVERT: D 203 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8182 (mtpt) REVERT: D 235 TYR cc_start: 0.7719 (t80) cc_final: 0.7332 (t80) REVERT: E 203 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8163 (mtpt) REVERT: F 52 LEU cc_start: 0.7850 (mt) cc_final: 0.7616 (mt) REVERT: F 128 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8456 (ttp-110) REVERT: F 282 ASN cc_start: 0.8659 (t0) cc_final: 0.8232 (m-40) REVERT: F 290 MET cc_start: 0.8026 (mtp) cc_final: 0.7764 (mtt) REVERT: G 235 TYR cc_start: 0.7697 (t80) cc_final: 0.7478 (t80) REVERT: G 282 ASN cc_start: 0.8687 (t0) cc_final: 0.8375 (t0) outliers start: 6 outliers final: 2 residues processed: 135 average time/residue: 0.1220 time to fit residues: 26.1348 Evaluate side-chains 115 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 17 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 ASN D 355 ASN E 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109466 restraints weight = 16810.839| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.74 r_work: 0.2993 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16583 Z= 0.110 Angle : 0.501 5.678 22421 Z= 0.250 Chirality : 0.037 0.123 2646 Planarity : 0.003 0.029 2625 Dihedral : 5.849 37.530 2359 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.74 % Allowed : 15.02 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1890 helix: 1.05 (0.14), residues: 1435 sheet: -2.54 (0.60), residues: 84 loop : -2.52 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.007 0.001 TYR E 215 PHE 0.006 0.001 PHE C 292 TRP 0.010 0.001 TRP G 74 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (16569) covalent geometry : angle 0.50002 / 0.25 (22393) SS BOND : bond 0.00092 / 0.04 ( 14) SS BOND : angle 1.03324 / 0.62 ( 28) hydrogen bonds : bond 0.03745 / 2.49 ( 966) hydrogen bonds : angle 3.31965 / 2.37 ( 2856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8579 (ttp80) REVERT: B 203 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8341 (ttpt) REVERT: B 290 MET cc_start: 0.7824 (mtp) cc_final: 0.7543 (mtt) REVERT: D 312 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8312 (mt-10) REVERT: E 203 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8383 (ttpt) REVERT: E 244 ASP cc_start: 0.7225 (p0) cc_final: 0.6788 (p0) REVERT: F 52 LEU cc_start: 0.7859 (mt) cc_final: 0.7558 (mt) REVERT: F 235 TYR cc_start: 0.7676 (t80) cc_final: 0.7383 (t80) REVERT: F 290 MET cc_start: 0.8086 (mtp) cc_final: 0.7835 (mtt) REVERT: G 282 ASN cc_start: 0.8661 (t0) cc_final: 0.8326 (t0) outliers start: 13 outliers final: 11 residues processed: 128 average time/residue: 0.1219 time to fit residues: 24.7215 Evaluate side-chains 115 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 142 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 0.0060 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 121 optimal weight: 0.0010 chunk 60 optimal weight: 0.8980 overall best weight: 0.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN G 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108699 restraints weight = 16724.884| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.73 r_work: 0.2981 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16583 Z= 0.115 Angle : 0.494 5.627 22421 Z= 0.247 Chirality : 0.037 0.122 2646 Planarity : 0.003 0.028 2625 Dihedral : 5.673 36.392 2359 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.64 % Allowed : 15.42 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1890 helix: 1.42 (0.14), residues: 1435 sheet: -2.44 (0.62), residues: 84 loop : -2.37 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.008 0.001 TYR E 215 PHE 0.006 0.001 PHE C 349 TRP 0.008 0.001 TRP D 74 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (16569) covalent geometry : angle 0.49284 / 0.25 (22393) SS BOND : bond 0.00105 / 0.06 ( 14) SS BOND : angle 1.02847 / 0.62 ( 28) hydrogen bonds : bond 0.03687 / 2.45 ( 966) hydrogen bonds : angle 3.25097 / 2.32 ( 2856) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8616 (ttp80) REVERT: B 290 MET cc_start: 0.7875 (mtp) cc_final: 0.7587 (mtt) REVERT: D 235 TYR cc_start: 0.7935 (t80) cc_final: 0.7649 (t80) REVERT: E 29 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: E 203 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8384 (ttpt) REVERT: E 244 ASP cc_start: 0.7240 (p0) cc_final: 0.6841 (p0) REVERT: F 29 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6043 (mtt180) REVERT: F 235 TYR cc_start: 0.7724 (t80) cc_final: 0.7409 (t80) REVERT: F 290 MET cc_start: 0.8091 (mtp) cc_final: 0.7858 (mtt) outliers start: 29 outliers final: 21 residues processed: 125 average time/residue: 0.1301 time to fit residues: 24.7400 Evaluate side-chains 124 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 154 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 156 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.0470 chunk 90 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.145065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112022 restraints weight = 16653.113| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.69 r_work: 0.3038 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16583 Z= 0.094 Angle : 0.464 5.549 22421 Z= 0.231 Chirality : 0.036 0.120 2646 Planarity : 0.003 0.044 2625 Dihedral : 5.189 31.868 2359 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.96 % Allowed : 16.04 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1890 helix: 1.73 (0.15), residues: 1435 sheet: -2.43 (0.62), residues: 84 loop : -2.18 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.007 0.000 TYR A 215 PHE 0.005 0.001 PHE C 126 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (16569) covalent geometry : angle 0.46316 / 0.23 (22393) SS BOND : bond 0.00085 / 0.04 ( 14) SS BOND : angle 1.08287 / 0.66 ( 28) hydrogen bonds : bond 0.03219 / 2.14 ( 966) hydrogen bonds : angle 3.10852 / 2.22 ( 2856) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5928 (mtt180) REVERT: B 203 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8415 (ttpt) REVERT: B 290 MET cc_start: 0.7777 (mtp) cc_final: 0.7542 (mtt) REVERT: C 29 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6405 (mtt180) REVERT: D 235 TYR cc_start: 0.7927 (t80) cc_final: 0.7589 (t80) REVERT: E 29 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7070 (mtt-85) REVERT: E 203 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8326 (ttpt) REVERT: E 244 ASP cc_start: 0.7029 (p0) cc_final: 0.6671 (p0) REVERT: F 235 TYR cc_start: 0.7724 (t80) cc_final: 0.7402 (t80) REVERT: F 290 MET cc_start: 0.7952 (mtp) cc_final: 0.7745 (mtt) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.1329 time to fit residues: 22.7717 Evaluate side-chains 110 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 127 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.104407 restraints weight = 16855.506| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.70 r_work: 0.2922 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16583 Z= 0.178 Angle : 0.558 5.856 22421 Z= 0.278 Chirality : 0.040 0.132 2646 Planarity : 0.003 0.028 2625 Dihedral : 5.974 38.065 2359 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.76 % Allowed : 16.50 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1890 helix: 1.60 (0.14), residues: 1428 sheet: -2.50 (0.61), residues: 84 loop : -2.19 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.010 0.001 TYR E 280 PHE 0.009 0.001 PHE G 349 TRP 0.012 0.002 TRP A 127 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (16569) covalent geometry : angle 0.55734 / 0.28 (22393) SS BOND : bond 0.00199 / 0.11 ( 14) SS BOND : angle 1.03413 / 0.63 ( 28) hydrogen bonds : bond 0.04507 / 2.99 ( 966) hydrogen bonds : angle 3.38889 / 2.42 ( 2856) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8589 (ttp80) REVERT: B 290 MET cc_start: 0.7964 (mtp) cc_final: 0.7636 (mtt) REVERT: D 235 TYR cc_start: 0.7970 (t80) cc_final: 0.7664 (t80) REVERT: E 29 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7421 (mtm-85) REVERT: E 244 ASP cc_start: 0.7284 (p0) cc_final: 0.6833 (p0) REVERT: F 235 TYR cc_start: 0.7834 (t80) cc_final: 0.7578 (t80) REVERT: G 31 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7663 (mt-10) REVERT: G 309 LYS cc_start: 0.8265 (mtpp) cc_final: 0.8056 (mtpp) outliers start: 31 outliers final: 25 residues processed: 132 average time/residue: 0.1281 time to fit residues: 26.0529 Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 282 ASN F 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109271 restraints weight = 16547.042| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.69 r_work: 0.3000 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16583 Z= 0.104 Angle : 0.474 5.528 22421 Z= 0.236 Chirality : 0.037 0.120 2646 Planarity : 0.003 0.026 2625 Dihedral : 5.354 35.387 2359 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.02 % Allowed : 18.20 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.21), residues: 1890 helix: 1.87 (0.15), residues: 1435 sheet: -2.53 (0.61), residues: 84 loop : -2.02 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 29 TYR 0.007 0.001 TYR A 215 PHE 0.005 0.001 PHE C 109 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (16569) covalent geometry : angle 0.47249 / 0.24 (22393) SS BOND : bond 0.00083 / 0.04 ( 14) SS BOND : angle 1.05705 / 0.64 ( 28) hydrogen bonds : bond 0.03451 / 2.29 ( 966) hydrogen bonds : angle 3.17967 / 2.27 ( 2856) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5837 (mtt180) REVERT: B 290 MET cc_start: 0.7855 (mtp) cc_final: 0.7567 (mtt) REVERT: C 29 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6550 (mtt180) REVERT: D 235 TYR cc_start: 0.7969 (t80) cc_final: 0.7639 (t80) REVERT: E 29 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7301 (mtm-85) REVERT: E 203 LYS cc_start: 0.8578 (mmmm) cc_final: 0.8308 (ttpt) REVERT: E 244 ASP cc_start: 0.7095 (p0) cc_final: 0.6637 (p0) REVERT: F 235 TYR cc_start: 0.7852 (t80) cc_final: 0.7581 (t80) REVERT: G 309 LYS cc_start: 0.8206 (mtpp) cc_final: 0.8005 (mtpp) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.1293 time to fit residues: 23.1095 Evaluate side-chains 114 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 0.0770 chunk 147 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109714 restraints weight = 16649.877| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.71 r_work: 0.3000 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16583 Z= 0.100 Angle : 0.471 5.531 22421 Z= 0.234 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.034 2625 Dihedral : 5.201 34.523 2359 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.13 % Allowed : 18.65 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1890 helix: 2.00 (0.15), residues: 1435 sheet: -2.62 (0.59), residues: 84 loop : -1.93 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.008 0.001 TYR E 280 PHE 0.006 0.001 PHE C 126 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (16569) covalent geometry : angle 0.46933 / 0.23 (22393) SS BOND : bond 0.00084 / 0.04 ( 14) SS BOND : angle 1.05912 / 0.65 ( 28) hydrogen bonds : bond 0.03365 / 2.23 ( 966) hydrogen bonds : angle 3.11436 / 2.22 ( 2856) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.5812 (mtt180) REVERT: B 128 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8581 (ttp80) REVERT: B 290 MET cc_start: 0.7870 (mtp) cc_final: 0.7587 (mtt) REVERT: C 29 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6369 (mtt180) REVERT: D 235 TYR cc_start: 0.7971 (t80) cc_final: 0.7630 (t80) REVERT: E 203 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8376 (ttpt) REVERT: E 244 ASP cc_start: 0.7081 (p0) cc_final: 0.6605 (p0) REVERT: E 297 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8231 (mtm) REVERT: F 235 TYR cc_start: 0.7859 (t80) cc_final: 0.7604 (t80) REVERT: G 31 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7575 (mt-10) REVERT: G 143 MET cc_start: 0.8206 (mtt) cc_final: 0.7864 (mtt) REVERT: G 309 LYS cc_start: 0.8203 (mtpp) cc_final: 0.8002 (mtpp) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1285 time to fit residues: 22.4012 Evaluate side-chains 120 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.0030 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 ASN E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107087 restraints weight = 16612.080| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.73 r_work: 0.2964 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16583 Z= 0.124 Angle : 0.497 5.572 22421 Z= 0.247 Chirality : 0.038 0.122 2646 Planarity : 0.003 0.035 2625 Dihedral : 5.360 36.080 2359 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.19 % Allowed : 19.05 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1890 helix: 1.97 (0.15), residues: 1428 sheet: -2.63 (0.58), residues: 84 loop : -1.96 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.008 0.001 TYR A 215 PHE 0.008 0.001 PHE B 333 TRP 0.008 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (16569) covalent geometry : angle 0.49561 / 0.25 (22393) SS BOND : bond 0.00111 / 0.06 ( 14) SS BOND : angle 1.02741 / 0.62 ( 28) hydrogen bonds : bond 0.03762 / 2.49 ( 966) hydrogen bonds : angle 3.17771 / 2.27 ( 2856) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8391 (mt-10) REVERT: B 29 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.5840 (mtt180) REVERT: B 290 MET cc_start: 0.7918 (mtp) cc_final: 0.7591 (mtt) REVERT: D 28 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8094 (mp) REVERT: D 235 TYR cc_start: 0.8004 (t80) cc_final: 0.7694 (t80) REVERT: E 203 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8386 (ttpt) REVERT: E 244 ASP cc_start: 0.7149 (p0) cc_final: 0.6666 (p0) REVERT: F 235 TYR cc_start: 0.7860 (t80) cc_final: 0.7604 (t80) REVERT: G 31 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7587 (mt-10) REVERT: G 309 LYS cc_start: 0.8213 (mtpp) cc_final: 0.8006 (mtpp) outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.1242 time to fit residues: 23.1761 Evaluate side-chains 124 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 127 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 ASN C 355 ASN E 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.143290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.110004 restraints weight = 16675.336| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.71 r_work: 0.3005 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16583 Z= 0.097 Angle : 0.468 5.517 22421 Z= 0.232 Chirality : 0.036 0.120 2646 Planarity : 0.003 0.034 2625 Dihedral : 5.125 33.891 2359 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.13 % Allowed : 19.44 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.21), residues: 1890 helix: 2.09 (0.15), residues: 1435 sheet: -2.62 (0.58), residues: 84 loop : -1.83 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.007 0.001 TYR A 215 PHE 0.006 0.001 PHE C 126 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (16569) covalent geometry : angle 0.46683 / 0.23 (22393) SS BOND : bond 0.00085 / 0.04 ( 14) SS BOND : angle 1.04388 / 0.64 ( 28) hydrogen bonds : bond 0.03315 / 2.20 ( 966) hydrogen bonds : angle 3.09882 / 2.21 ( 2856) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.5700 (mtt180) REVERT: B 290 MET cc_start: 0.7859 (mtp) cc_final: 0.7587 (mtt) REVERT: C 29 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6338 (mtt180) REVERT: D 235 TYR cc_start: 0.7940 (t80) cc_final: 0.7640 (t80) REVERT: E 203 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8384 (ttpt) REVERT: E 244 ASP cc_start: 0.7074 (p0) cc_final: 0.6590 (p0) REVERT: E 297 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (mtm) REVERT: F 235 TYR cc_start: 0.7874 (t80) cc_final: 0.7611 (t80) REVERT: G 31 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7572 (mt-10) REVERT: G 143 MET cc_start: 0.8203 (mtt) cc_final: 0.7878 (mtt) REVERT: G 309 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7966 (mtpp) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 0.1225 time to fit residues: 22.3016 Evaluate side-chains 124 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 74 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 144 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 ASN E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.142980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109812 restraints weight = 16644.010| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.70 r_work: 0.3007 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16583 Z= 0.101 Angle : 0.471 5.530 22421 Z= 0.234 Chirality : 0.037 0.120 2646 Planarity : 0.003 0.033 2625 Dihedral : 5.077 33.187 2359 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.25 % Allowed : 19.39 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.21), residues: 1890 helix: 2.13 (0.15), residues: 1428 sheet: -2.57 (0.58), residues: 84 loop : -1.90 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.006 0.001 TYR F 215 PHE 0.006 0.001 PHE C 126 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (16569) covalent geometry : angle 0.46976 / 0.23 (22393) SS BOND : bond 0.00086 / 0.04 ( 14) SS BOND : angle 1.03283 / 0.63 ( 28) hydrogen bonds : bond 0.03356 / 2.22 ( 966) hydrogen bonds : angle 3.07289 / 2.19 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3399.37 seconds wall clock time: 59 minutes 15.77 seconds (3555.77 seconds total)