Starting phenix.real_space_refine on Sun Aug 24 02:42:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_20964.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_20964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_20964.map" model { file = "/net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_20964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzy_20964/08_2025/6uzy_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 27 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: 27 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: 27 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: 27 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: 27 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: 27 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: 27 Planarities with less than four sites: {'6OU:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.47, per 1000 atoms: 0.21 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 565.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.41 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: 1.72 Time building geometry restraints manager: 1.39 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 - 32.10: 9576 32.10 - 64.21: 336 64.21 - 96.31: 21 96.31 - 128.41: 0 128.41 - 160.52: 21 Dihedral angle restraints: 9954 sinusoidal: 4123 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 9951 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: 0.03 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.220 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 17.598 160.518 6118 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 aren 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 covalent geometry : bond 0.01168 (16569) covalent geometry : angle 1.09667 (22393) SS BOND : bond 0.00360 ( 14) SS BOND : angle 1.18104 ( 28) hydrogen bonds : bond 0.13525 ( 966) hydrogen bonds : angle 5.70692 ( 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 : 0.599 Fit side-chains REVERT: B 52 LEU cc_start: 0.7829 (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: 0.7276 (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: 0.7588 (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: 0.1220 time to fit residues: 27.1512 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 : 0.400 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3553 r_free = 0.3553 target = 0.144588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110980 restraints weight = 16529.871| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.73 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: 0.7750 moved from start: 0.1363 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 : 0.518 5.879 22421 Z= 0.261 Chirality : 0.037 0.124 2646 Planarity : 0.004 0.031 2625 Dihedral : 11.013 106.939 2415 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.23 % Allowed : 11.05 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 1890 helix: 0.30 (0.14), residues: 1435 sheet: -2.42 (0.45), residues: 119 loop : -3.00 (0.29), residues: 336 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 0.001 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00224 (16569) covalent geometry : angle 0.51653 (22393) SS BOND : bond 0.00145 ( 14) SS BOND : angle 1.23436 ( 28) hydrogen bonds : bond 0.03762 ( 966) hydrogen bonds : angle 3.63154 ( 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 136 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.524 Fit side-chains REVERT: A 203 LYS cc_start: 0.8252 (mmmm) cc_final: 0.8025 (mtpt) REVERT: B 128 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8571 (ttp80) REVERT: B 290 MET cc_start: 0.7786 (mtp) cc_final: 0.7539 (mtt) REVERT: D 235 TYR cc_start: 0.7711 (t80) cc_final: 0.7324 (t80) REVERT: E 203 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8154 (mtpt) REVERT: F 52 LEU cc_start: 0.7850 (mt) cc_final: 0.7613 (mt) REVERT: F 128 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8449 (ttp-110) REVERT: F 282 ASN cc_start: 0.8661 (t0) cc_final: 0.8234 (m-40) REVERT: F 290 MET cc_start: 0.8026 (mtp) cc_final: 0.7767 (mtt) REVERT: G 235 TYR cc_start: 0.7695 (t80) cc_final: 0.7479 (t80) REVERT: G 282 ASN cc_start: 0.8692 (t0) cc_final: 0.8377 (t0) outliers start: 4 outliers final: 0 residues processed: 135 average time/residue: 0.1049 time to fit residues: 22.1544 Evaluate side-chains 112 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 17 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 185 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 162 optimal weight: 0.5980 chunk 166 optimal weight: 0.0970 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 282 ASN G 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.147855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114748 restraints weight = 16662.322| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.73 r_work: 0.3071 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1890 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= 0.092 Angle : 0.474 5.629 22421 Z= 0.235 Chirality : 0.036 0.122 2646 Planarity : 0.003 0.030 2625 Dihedral : 9.002 99.348 2415 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.45 % Allowed : 14.00 % Favored : 85.54 % 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 aren not related in a simple way. whole: 0.35 (0.20), residues: 1890 helix: 1.12 (0.14), residues: 1435 sheet: -2.57 (0.59), residues: 84 loop : -2.50 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.006 0.000 TYR B 215 PHE 0.004 0.000 PHE C 126 TRP 0.009 0.001 TRP D 74 HIS 0.001 0.000 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00189 (16569) covalent geometry : angle 0.47275 (22393) SS BOND : bond 0.00077 ( 14) SS BOND : angle 1.07216 ( 28) hydrogen bonds : bond 0.03174 ( 966) hydrogen bonds : angle 3.26197 ( 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 138 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8146 (ttpt) REVERT: A 239 LEU cc_start: 0.8295 (tp) cc_final: 0.8090 (tp) REVERT: B 128 ARG cc_start: 0.8788 (ttm170) cc_final: 0.8558 (ttp80) REVERT: B 203 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8308 (ttpt) REVERT: D 312 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8280 (mt-10) REVERT: E 203 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8214 (ttpt) REVERT: E 244 ASP cc_start: 0.7203 (p0) cc_final: 0.6789 (p0) REVERT: F 52 LEU cc_start: 0.7944 (mt) cc_final: 0.7655 (mt) REVERT: F 235 TYR cc_start: 0.7657 (t80) cc_final: 0.7337 (t80) REVERT: F 350 LEU cc_start: 0.8539 (mt) cc_final: 0.8322 (mp) REVERT: G 350 LEU cc_start: 0.8745 (mt) cc_final: 0.8464 (mt) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.1137 time to fit residues: 23.0744 Evaluate side-chains 118 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 CYS Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain D residue 203 LYS 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 G residue 70 THR 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: 9.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 121 optimal weight: 0.0020 chunk 60 optimal weight: 0.2980 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.141366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108005 restraints weight = 16681.249| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.70 r_work: 0.2969 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1885 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= 0.134 Angle : 0.522 5.695 22421 Z= 0.260 Chirality : 0.038 0.124 2646 Planarity : 0.003 0.030 2625 Dihedral : 9.267 106.841 2415 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 15.31 % Favored : 83.11 % 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 aren not related in a simple way. whole: 0.70 (0.21), residues: 1890 helix: 1.42 (0.14), residues: 1428 sheet: -2.52 (0.61), residues: 84 loop : -2.49 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 128 TYR 0.012 0.001 TYR E 280 PHE 0.008 0.001 PHE B 333 TRP 0.009 0.001 TRP B 127 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00324 (16569) covalent geometry : angle 0.52114 (22393) SS BOND : bond 0.00112 ( 14) SS BOND : angle 1.02607 ( 28) hydrogen bonds : bond 0.04036 ( 966) hydrogen bonds : angle 3.26258 ( 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 135 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6152 (mtt180) REVERT: B 29 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.5882 (mtt180) REVERT: B 128 ARG cc_start: 0.8811 (ttm170) cc_final: 0.8596 (ttp80) REVERT: C 29 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6256 (mtt180) REVERT: C 350 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 203 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8157 (ttmt) REVERT: D 235 TYR cc_start: 0.7871 (t80) cc_final: 0.7534 (t80) REVERT: D 312 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8350 (mt-10) REVERT: E 203 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8378 (ttpt) REVERT: E 244 ASP cc_start: 0.7244 (p0) cc_final: 0.6782 (p0) REVERT: F 29 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.5978 (mtt180) REVERT: F 128 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8524 (ttp-110) REVERT: F 235 TYR cc_start: 0.7701 (t80) cc_final: 0.7413 (t80) REVERT: G 29 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6630 (mtt180) outliers start: 28 outliers final: 14 residues processed: 128 average time/residue: 0.1304 time to fit residues: 24.0048 Evaluate side-chains 123 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 154 ILE 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 231 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 203 LYS 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 29 ARG 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 29 ARG Chi-restraints excluded: chain G residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 156 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN E 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110138 restraints weight = 16657.769| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.71 r_work: 0.3007 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2111 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= 0.102 Angle : 0.483 6.577 22421 Z= 0.239 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.935 106.969 2415 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.36 % Allowed : 16.04 % Favored : 82.60 % 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 aren not related in a simple way. whole: 1.12 (0.21), residues: 1890 helix: 1.69 (0.15), residues: 1435 sheet: -2.47 (0.62), residues: 84 loop : -2.24 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.007 0.001 TYR A 215 PHE 0.015 0.001 PHE F 240 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00234 (16569) covalent geometry : angle 0.48206 (22393) SS BOND : bond 0.00078 ( 14) SS BOND : angle 1.06138 ( 28) hydrogen bonds : bond 0.03469 ( 966) hydrogen bonds : angle 3.16219 ( 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 127 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.5799 (mtt180) REVERT: B 128 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8562 (ttp80) REVERT: C 350 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8353 (mm) REVERT: D 203 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: D 235 TYR cc_start: 0.7955 (t80) cc_final: 0.7629 (t80) REVERT: D 312 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8261 (mt-10) REVERT: E 244 ASP cc_start: 0.7184 (p0) cc_final: 0.6814 (p0) REVERT: F 128 ARG cc_start: 0.8786 (ttp80) cc_final: 0.8571 (ttp-110) REVERT: F 235 TYR cc_start: 0.7738 (t80) cc_final: 0.7457 (t80) REVERT: G 29 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6014 (mtt180) REVERT: G 31 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7453 (mt-10) outliers start: 24 outliers final: 18 residues processed: 117 average time/residue: 0.1181 time to fit residues: 21.2883 Evaluate side-chains 118 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 70 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 154 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 Chi-restraints excluded: chain G residue 297 MET 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: 0.8980 chunk 96 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3528 r_free = 0.3528 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109629 restraints weight = 16594.206| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.69 r_work: 0.3000 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2197 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= 0.108 Angle : 0.486 5.998 22421 Z= 0.240 Chirality : 0.037 0.122 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.896 108.146 2415 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.47 % Allowed : 16.33 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.21), residues: 1890 helix: 1.87 (0.15), residues: 1428 sheet: -2.43 (0.62), residues: 84 loop : -2.22 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.007 0.001 TYR A 215 PHE 0.011 0.001 PHE F 240 TRP 0.008 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00251 (16569) covalent geometry : angle 0.48498 (22393) SS BOND : bond 0.00083 ( 14) SS BOND : angle 1.06522 ( 28) hydrogen bonds : bond 0.03534 ( 966) hydrogen bonds : angle 3.13516 ( 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 127 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6543 (mtt180) REVERT: B 29 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5820 (mtt180) REVERT: B 128 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8556 (ttp80) REVERT: C 350 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (mm) REVERT: D 203 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8229 (ttmt) REVERT: D 235 TYR cc_start: 0.7989 (t80) cc_final: 0.7669 (t80) REVERT: E 244 ASP cc_start: 0.7201 (p0) cc_final: 0.6734 (p0) REVERT: F 29 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5953 (mtt180) REVERT: F 128 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8566 (ttp-110) REVERT: F 235 TYR cc_start: 0.7808 (t80) cc_final: 0.7544 (t80) REVERT: G 29 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6022 (mtt180) REVERT: G 31 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7495 (mt-10) outliers start: 26 outliers final: 18 residues processed: 119 average time/residue: 0.1301 time to fit residues: 22.9348 Evaluate side-chains 123 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 154 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3534 r_free = 0.3534 target = 0.143449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110227 restraints weight = 16485.993| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.69 r_work: 0.3014 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2278 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= 0.103 Angle : 0.478 6.288 22421 Z= 0.236 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.822 108.801 2415 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.70 % Allowed : 16.84 % Favored : 81.46 % 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 aren not related in a simple way. whole: 1.50 (0.21), residues: 1890 helix: 1.99 (0.15), residues: 1428 sheet: -2.46 (0.62), residues: 84 loop : -2.13 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.007 0.001 TYR A 215 PHE 0.010 0.001 PHE F 240 TRP 0.008 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00236 (16569) covalent geometry : angle 0.47708 (22393) SS BOND : bond 0.00083 ( 14) SS BOND : angle 1.07433 ( 28) hydrogen bonds : bond 0.03415 ( 966) hydrogen bonds : angle 3.09174 ( 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 133 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6124 (mtt180) REVERT: B 128 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8528 (ttp80) REVERT: B 297 MET cc_start: 0.8820 (mtm) cc_final: 0.8584 (mtp) REVERT: C 29 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6639 (mtt180) REVERT: C 350 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8338 (mm) REVERT: D 203 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8220 (ttmt) REVERT: D 235 TYR cc_start: 0.7962 (t80) cc_final: 0.7637 (t80) REVERT: E 244 ASP cc_start: 0.7069 (p0) cc_final: 0.6602 (p0) REVERT: F 29 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.5991 (mtt180) REVERT: F 128 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8555 (ttp-110) REVERT: F 235 TYR cc_start: 0.7842 (t80) cc_final: 0.7557 (t80) REVERT: G 29 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.5942 (mtt180) REVERT: G 31 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7456 (mt-10) outliers start: 30 outliers final: 23 residues processed: 124 average time/residue: 0.1263 time to fit residues: 23.3861 Evaluate side-chains 128 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 C residue 350 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU 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 82 SER Chi-restraints excluded: chain G residue 154 ILE 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: 7.9990 chunk 147 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3534 r_free = 0.3534 target = 0.143356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110238 restraints weight = 16627.013| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.69 r_work: 0.3014 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2334 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= 0.103 Angle : 0.477 6.256 22421 Z= 0.235 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.797 109.348 2415 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.87 % Allowed : 17.12 % Favored : 81.01 % 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 aren not related in a simple way. whole: 1.61 (0.21), residues: 1890 helix: 2.06 (0.15), residues: 1428 sheet: -2.45 (0.62), residues: 84 loop : -2.06 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.007 0.001 TYR A 215 PHE 0.009 0.001 PHE F 240 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00238 (16569) covalent geometry : angle 0.47623 (22393) SS BOND : bond 0.00084 ( 14) SS BOND : angle 1.07721 ( 28) hydrogen bonds : bond 0.03405 ( 966) hydrogen bonds : angle 3.08088 ( 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 136 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6127 (mtt180) REVERT: B 29 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.5899 (mtt180) REVERT: B 128 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8525 (ttp80) REVERT: B 297 MET cc_start: 0.8787 (mtm) cc_final: 0.8542 (mtp) REVERT: C 29 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6850 (mtt180) REVERT: C 350 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8324 (mm) REVERT: D 203 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: D 235 TYR cc_start: 0.7950 (t80) cc_final: 0.7614 (t80) REVERT: E 244 ASP cc_start: 0.7065 (p0) cc_final: 0.6579 (p0) REVERT: F 29 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6080 (mtt180) REVERT: F 128 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8554 (ttp-110) REVERT: F 235 TYR cc_start: 0.7839 (t80) cc_final: 0.7558 (t80) REVERT: G 29 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.5946 (mtt180) REVERT: G 31 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7453 (mt-10) outliers start: 33 outliers final: 25 residues processed: 126 average time/residue: 0.1310 time to fit residues: 24.6444 Evaluate side-chains 133 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 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 C residue 350 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU 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 Chi-restraints excluded: chain G residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN G 63 GLN 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 = 0.142525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109399 restraints weight = 16555.495| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.69 r_work: 0.2994 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2336 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= 0.114 Angle : 0.489 6.630 22421 Z= 0.241 Chirality : 0.037 0.122 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.865 110.722 2415 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.76 % Allowed : 17.52 % Favored : 80.73 % 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 aren not related in a simple way. whole: 1.60 (0.21), residues: 1890 helix: 2.05 (0.15), residues: 1428 sheet: -2.48 (0.61), residues: 84 loop : -2.05 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.008 0.001 TYR A 215 PHE 0.010 0.001 PHE F 240 TRP 0.009 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00270 (16569) covalent geometry : angle 0.48766 (22393) SS BOND : bond 0.00095 ( 14) SS BOND : angle 1.06579 ( 28) hydrogen bonds : bond 0.03565 ( 966) hydrogen bonds : angle 3.11401 ( 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 135 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6572 (mtt180) REVERT: B 29 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6003 (mtt180) REVERT: B 128 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8539 (ttp80) REVERT: B 297 MET cc_start: 0.8819 (mtm) cc_final: 0.8619 (mtp) REVERT: C 350 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8366 (mm) REVERT: D 203 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: D 235 TYR cc_start: 0.7974 (t80) cc_final: 0.7638 (t80) REVERT: E 244 ASP cc_start: 0.7090 (p0) cc_final: 0.6624 (p0) REVERT: F 29 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6136 (mtt180) REVERT: F 128 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8552 (ttp-110) REVERT: F 235 TYR cc_start: 0.7875 (t80) cc_final: 0.7585 (t80) REVERT: G 29 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6121 (mtt180) REVERT: G 31 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7528 (mt-10) outliers start: 31 outliers final: 25 residues processed: 126 average time/residue: 0.1417 time to fit residues: 26.4741 Evaluate side-chains 133 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 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 C residue 350 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU 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=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: 1.9990 chunk 148 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN F 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.109373 restraints weight = 16687.019| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.70 r_work: 0.2994 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2367 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= 0.112 Angle : 0.488 7.197 22421 Z= 0.241 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.876 111.445 2415 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.76 % Allowed : 17.57 % Favored : 80.67 % 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 aren not related in a simple way. whole: 1.63 (0.21), residues: 1890 helix: 2.07 (0.15), residues: 1428 sheet: -2.52 (0.61), residues: 84 loop : -2.02 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 128 TYR 0.007 0.001 TYR A 215 PHE 0.010 0.001 PHE F 240 TRP 0.009 0.001 TRP B 74 HIS 0.002 0.000 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00264 (16569) covalent geometry : angle 0.48635 (22393) SS BOND : bond 0.00087 ( 14) SS BOND : angle 1.07304 ( 28) hydrogen bonds : bond 0.03550 ( 966) hydrogen bonds : angle 3.11126 ( 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 136 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6333 (mtt180) REVERT: B 29 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.5992 (mtt180) REVERT: B 128 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8534 (ttp80) REVERT: C 350 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8355 (mm) REVERT: D 203 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8288 (ttmt) REVERT: D 235 TYR cc_start: 0.7970 (t80) cc_final: 0.7634 (t80) REVERT: E 244 ASP cc_start: 0.7091 (p0) cc_final: 0.6623 (p0) REVERT: F 29 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6112 (mtt180) REVERT: F 128 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8553 (ttp-110) REVERT: F 235 TYR cc_start: 0.7871 (t80) cc_final: 0.7579 (t80) REVERT: G 29 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6123 (mtt180) REVERT: G 31 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7516 (mt-10) outliers start: 31 outliers final: 25 residues processed: 127 average time/residue: 0.1396 time to fit residues: 26.2141 Evaluate side-chains 134 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG 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 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 C residue 350 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 350 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 74 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 107 optimal weight: 0.0030 chunk 179 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 144 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110836 restraints weight = 16596.867| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.69 r_work: 0.3015 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2433 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= 0.100 Angle : 0.474 7.048 22421 Z= 0.234 Chirality : 0.037 0.121 2646 Planarity : 0.003 0.028 2625 Dihedral : 8.796 111.396 2415 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.70 % Allowed : 17.86 % Favored : 80.44 % 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 aren not related in a simple way. whole: 1.73 (0.21), residues: 1890 helix: 2.15 (0.15), residues: 1428 sheet: -2.54 (0.60), residues: 84 loop : -1.99 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 29 TYR 0.007 0.001 TYR A 215 PHE 0.009 0.001 PHE F 240 TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00228 (16569) covalent geometry : angle 0.47235 (22393) SS BOND : bond 0.00078 ( 14) SS BOND : angle 1.07126 ( 28) hydrogen bonds : bond 0.03340 ( 966) hydrogen bonds : angle 3.06330 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.92 seconds wall clock time: 54 minutes 5.11 seconds (3245.11 seconds total)