Starting phenix.real_space_refine on Sun Jul 5 00:44:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j85_36060/07_2026/8j85_36060.cif" } resolution = 2.7 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= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 Cl 8 4.86 5 C 15288 2.51 5 N 4432 2.21 5 O 4560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24376 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24376 At special positions: 0 Unit cell: (145.35, 145.35, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 72 16.00 O 4560 8.00 N 4432 7.00 C 15288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.01 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.01 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.01 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.01 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.01 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.02 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 44.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP A 98 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.587A pdb=" N ALA A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.751A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.971A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.650A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.586A pdb=" N ASP B 98 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.585A pdb=" N ALA B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 293 through 305 removed outlier: 3.763A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.529A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.887A pdb=" N VAL B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 373 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.646A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP C 98 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 99 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 171 through 179 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 190 through 205 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.763A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 322 removed outlier: 4.548A pdb=" N LYS C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.887A pdb=" N VAL C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.650A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.586A pdb=" N ASP D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 171 through 179 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.584A pdb=" N ALA D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 276 through 287 Processing helix chain 'D' and resid 293 through 305 removed outlier: 3.763A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 322 removed outlier: 4.535A pdb=" N LYS D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 354 through 364 removed outlier: 3.888A pdb=" N VAL D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.648A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.588A pdb=" N ASP E 98 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.588A pdb=" N ALA E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 Processing helix chain 'E' and resid 276 through 287 Processing helix chain 'E' and resid 293 through 305 removed outlier: 3.751A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 354 through 364 removed outlier: 3.972A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 375 through 383 removed outlier: 3.650A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP F 98 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 171 through 179 Processing helix chain 'F' and resid 182 through 186 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.585A pdb=" N ALA F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 Processing helix chain 'F' and resid 276 through 287 Processing helix chain 'F' and resid 293 through 305 removed outlier: 3.763A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.529A pdb=" N THR F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 364 removed outlier: 3.887A pdb=" N VAL F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 375 through 383 removed outlier: 3.647A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 94 through 100 removed outlier: 3.587A pdb=" N ASP G 98 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 100 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 171 through 179 Processing helix chain 'G' and resid 182 through 186 Processing helix chain 'G' and resid 190 through 205 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 Processing helix chain 'G' and resid 276 through 287 Processing helix chain 'G' and resid 293 through 305 removed outlier: 3.762A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 322 removed outlier: 4.549A pdb=" N LYS G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 Processing helix chain 'G' and resid 354 through 364 removed outlier: 3.887A pdb=" N VAL G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 375 through 383 removed outlier: 3.650A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 94 through 100 removed outlier: 3.586A pdb=" N ASP H 98 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 120 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 171 through 179 Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'H' and resid 190 through 205 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.583A pdb=" N ALA H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 265 Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 293 through 305 removed outlier: 3.763A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 322 removed outlier: 4.536A pdb=" N LYS H 317 " --> pdb=" O VAL H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 Processing helix chain 'H' and resid 354 through 364 removed outlier: 3.887A pdb=" N VAL H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 373 Processing helix chain 'H' and resid 375 through 383 removed outlier: 3.649A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.577A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 45 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.577A pdb=" N GLN A 37 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.721A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 418 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.378A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP A 81 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 212 removed outlier: 6.554A pdb=" N ILE A 209 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS A 251 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 211 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 268 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.581A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 45 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.581A pdb=" N GLN B 37 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 13.343A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 418 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 84 removed outlier: 6.380A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 81 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.555A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 268 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 45 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN C 37 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 13.331A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.784A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.707A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 418 " --> pdb=" O TYR C 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 84 removed outlier: 6.379A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 81 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 212 removed outlier: 6.554A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 268 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 45 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN D 37 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.734A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.708A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 418 " --> pdb=" O TYR D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.379A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP D 81 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 209 through 212 removed outlier: 6.555A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 268 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.577A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 45 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.577A pdb=" N GLN E 37 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.720A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.696A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 418 " --> pdb=" O TYR E 425 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 84 removed outlier: 6.377A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP E 81 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 209 through 212 removed outlier: 6.553A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 268 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 45 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN F 37 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 13.343A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.789A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.684A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 418 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 84 removed outlier: 6.379A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP F 81 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 209 through 212 removed outlier: 6.554A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER F 268 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU G 45 " --> pdb=" O ARG G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN G 37 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY G 28 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP G 72 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N LEU G 30 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL G 74 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N ASP G 32 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N LEU G 76 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G 418 " --> pdb=" O TYR G 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 79 through 84 removed outlier: 6.379A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP G 81 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 209 through 212 removed outlier: 6.553A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 268 " --> pdb=" O VAL G 248 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU H 45 " --> pdb=" O ARG H 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.582A pdb=" N GLN H 37 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 13.341A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.733A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.720A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL H 418 " --> pdb=" O TYR H 425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 79 through 84 removed outlier: 6.379A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP H 81 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 209 through 212 removed outlier: 6.554A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 268 " --> pdb=" O VAL H 248 " (cutoff:3.500A) 1042 hydrogen bonds defined for protein. 2853 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: 5.20 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4176 1.31 - 1.44: 6600 1.44 - 1.56: 13960 1.56 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 24872 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 24867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 32820 2.18 - 4.36: 816 4.36 - 6.54: 84 6.54 - 8.73: 24 8.73 - 10.91: 8 Bond angle restraints: 33752 Sorted by residual: angle pdb=" N VAL E 132 " pdb=" CA VAL E 132 " pdb=" C VAL E 132 " ideal model delta sigma weight residual 113.53 105.76 7.77 9.80e-01 1.04e+00 6.29e+01 angle pdb=" N VAL A 132 " pdb=" CA VAL A 132 " pdb=" C VAL A 132 " ideal model delta sigma weight residual 113.53 105.81 7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" N VAL B 132 " pdb=" CA VAL B 132 " pdb=" C VAL B 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL F 132 " pdb=" CA VAL F 132 " pdb=" C VAL F 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 113.53 106.16 7.37 9.80e-01 1.04e+00 5.65e+01 ... (remaining 33747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 12606 17.28 - 34.55: 1481 34.55 - 51.83: 470 51.83 - 69.10: 139 69.10 - 86.38: 24 Dihedral angle restraints: 14720 sinusoidal: 5760 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY H 346 " pdb=" C GLY H 346 " pdb=" N VAL H 347 " pdb=" CA VAL H 347 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLY C 346 " pdb=" C GLY C 346 " pdb=" N VAL C 347 " pdb=" CA VAL C 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3058 0.066 - 0.132: 535 0.132 - 0.198: 77 0.198 - 0.264: 10 0.264 - 0.330: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U F 503 " pdb=" N 97U F 503 " pdb=" C 97U F 503 " pdb=" CB 97U F 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA 97U A 503 " pdb=" N 97U A 503 " pdb=" C 97U A 503 " pdb=" CB 97U A 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA 97U B 503 " pdb=" N 97U B 503 " pdb=" C 97U B 503 " pdb=" CB 97U B 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 3685 not shown) Planarity restraints: 4496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 73 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C LYS E 73 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS E 73 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 73 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LYS G 73 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL G 74 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 73 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LYS H 73 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS H 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL H 74 " -0.013 2.00e-02 2.50e+03 ... (remaining 4493 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 24 2.35 - 2.99: 12002 2.99 - 3.62: 33794 3.62 - 4.26: 57610 4.26 - 4.90: 99220 Nonbonded interactions: 202650 Sorted by model distance: nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.711 2.230 nonbonded pdb="ZN ZN F 502 " pdb=" OAX 97U F 503 " model vdw 1.712 2.230 nonbonded pdb="ZN ZN D 502 " pdb=" OAX 97U D 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN H 502 " pdb=" OAX 97U H 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.743 2.230 ... (remaining 202645 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.040 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.070 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 24912 Z= 0.382 Angle : 0.750 10.908 33768 Z= 0.447 Chirality : 0.054 0.330 3688 Planarity : 0.005 0.040 4496 Dihedral : 17.112 86.381 9016 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 18.87 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.14), residues: 3136 helix: 0.69 (0.15), residues: 1208 sheet: 0.51 (0.26), residues: 400 loop : -1.51 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 199 TYR 0.009 0.001 TYR E 333 PHE 0.011 0.001 PHE F 299 TRP 0.003 0.001 TRP E 79 HIS 0.007 0.001 HIS H 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.38 (24872) covalent geometry : angle 0.74903 / 0.45 (33752) SS BOND : bond 0.01736 / 1.08 ( 8) SS BOND : angle 1.89642 / 1.27 ( 16) hydrogen bonds : bond 0.15791 / 11.05 ( 1034) hydrogen bonds : angle 6.45987 / 4.64 ( 2853) metal coordination : bond 0.02663 / 1.65 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 467 time to evaluate : 0.982 Fit side-chains REVERT: A 23 VAL cc_start: 0.7512 (t) cc_final: 0.7286 (p) REVERT: A 76 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 315 ARG cc_start: 0.7221 (ttt90) cc_final: 0.6972 (mtp-110) REVERT: B 76 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7027 (tt) REVERT: B 315 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6992 (mtp-110) REVERT: C 315 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6988 (mtp-110) REVERT: D 23 VAL cc_start: 0.7542 (t) cc_final: 0.7298 (p) REVERT: D 76 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 315 ARG cc_start: 0.7278 (ttt90) cc_final: 0.7017 (mtp-110) REVERT: E 23 VAL cc_start: 0.7401 (t) cc_final: 0.6840 (p) REVERT: E 93 GLN cc_start: 0.7613 (mp10) cc_final: 0.7241 (mm-40) REVERT: E 281 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7213 (ttm110) REVERT: E 385 ASP cc_start: 0.7465 (p0) cc_final: 0.7129 (p0) REVERT: E 397 ASP cc_start: 0.7632 (m-30) cc_final: 0.7389 (m-30) REVERT: F 23 VAL cc_start: 0.7642 (t) cc_final: 0.7063 (p) REVERT: F 93 GLN cc_start: 0.7566 (mp10) cc_final: 0.7214 (mm-40) REVERT: F 385 ASP cc_start: 0.7481 (p0) cc_final: 0.7180 (p0) REVERT: F 397 ASP cc_start: 0.7617 (m-30) cc_final: 0.7370 (m-30) REVERT: G 23 VAL cc_start: 0.7427 (t) cc_final: 0.6918 (p) REVERT: G 93 GLN cc_start: 0.7546 (mp10) cc_final: 0.7198 (mm-40) REVERT: G 275 MET cc_start: 0.9094 (ttm) cc_final: 0.8882 (ttp) REVERT: G 385 ASP cc_start: 0.7437 (p0) cc_final: 0.7127 (p0) REVERT: G 397 ASP cc_start: 0.7609 (m-30) cc_final: 0.7381 (m-30) REVERT: H 23 VAL cc_start: 0.7421 (t) cc_final: 0.6866 (p) REVERT: H 93 GLN cc_start: 0.7587 (mp10) cc_final: 0.7233 (mm-40) REVERT: H 385 ASP cc_start: 0.7475 (p0) cc_final: 0.7126 (p0) REVERT: H 397 ASP cc_start: 0.7616 (m-30) cc_final: 0.7381 (m-30) outliers start: 32 outliers final: 5 residues processed: 493 average time/residue: 0.9150 time to fit residues: 501.1790 Evaluate side-chains 249 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 353 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.1980 overall best weight: 1.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 HIS H 163 HIS ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126535 restraints weight = 25439.545| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.68 r_work: 0.3432 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24912 Z= 0.142 Angle : 0.534 7.382 33768 Z= 0.281 Chirality : 0.046 0.230 3688 Planarity : 0.005 0.046 4496 Dihedral : 5.380 52.870 3671 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 21.27 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3136 helix: 1.12 (0.15), residues: 1232 sheet: 0.60 (0.25), residues: 400 loop : -1.27 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 355 TYR 0.010 0.001 TYR C 95 PHE 0.010 0.001 PHE F 294 TRP 0.005 0.001 TRP E 79 HIS 0.007 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24872) covalent geometry : angle 0.53339 / 0.28 (33752) SS BOND : bond 0.00206 / 0.11 ( 8) SS BOND : angle 1.19311 / 0.65 ( 16) hydrogen bonds : bond 0.04632 / 3.20 ( 1034) hydrogen bonds : angle 4.40357 / 3.23 ( 2853) metal coordination : bond 0.00516 / 0.36 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 1.032 Fit side-chains REVERT: A 315 ARG cc_start: 0.7292 (ttt90) cc_final: 0.6949 (mtp-110) REVERT: B 172 GLU cc_start: 0.7874 (tp30) cc_final: 0.6953 (tm-30) REVERT: B 312 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7117 (tp30) REVERT: B 315 ARG cc_start: 0.7320 (ttt90) cc_final: 0.6940 (mtp-110) REVERT: C 31 PHE cc_start: 0.8290 (t80) cc_final: 0.7869 (t80) REVERT: C 315 ARG cc_start: 0.7284 (ttt90) cc_final: 0.6921 (mtp-110) REVERT: D 172 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: D 315 ARG cc_start: 0.7249 (ttt90) cc_final: 0.6869 (mtp-110) REVERT: E 93 GLN cc_start: 0.7461 (mp10) cc_final: 0.6948 (mm-40) REVERT: E 173 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6024 (ttm170) REVERT: E 283 MET cc_start: 0.8777 (mtp) cc_final: 0.8478 (mtp) REVERT: E 338 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7318 (mtt180) REVERT: E 385 ASP cc_start: 0.8126 (p0) cc_final: 0.7857 (p0) REVERT: F 93 GLN cc_start: 0.7505 (mp10) cc_final: 0.6948 (mm-40) REVERT: F 173 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6102 (ttm170) REVERT: F 338 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7296 (mtt180) REVERT: F 385 ASP cc_start: 0.8077 (p0) cc_final: 0.7811 (p0) REVERT: G 93 GLN cc_start: 0.7427 (mp10) cc_final: 0.6889 (mm-40) REVERT: G 173 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6013 (ttm170) REVERT: G 283 MET cc_start: 0.8784 (mtp) cc_final: 0.8491 (mtp) REVERT: G 338 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: G 385 ASP cc_start: 0.8078 (p0) cc_final: 0.7819 (p0) REVERT: H 88 GLU cc_start: 0.7556 (pt0) cc_final: 0.7350 (pt0) REVERT: H 93 GLN cc_start: 0.7475 (mp10) cc_final: 0.6930 (mm-40) REVERT: H 173 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6181 (ttm170) REVERT: H 338 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7328 (mtt180) REVERT: H 385 ASP cc_start: 0.8058 (p0) cc_final: 0.7819 (p0) outliers start: 51 outliers final: 18 residues processed: 297 average time/residue: 0.7598 time to fit residues: 255.9235 Evaluate side-chains 247 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 34 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS E 271 HIS E 335 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120880 restraints weight = 25771.236| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.78 r_work: 0.3377 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.043 24912 Z= 0.363 Angle : 0.617 9.204 33768 Z= 0.326 Chirality : 0.050 0.234 3688 Planarity : 0.005 0.053 4496 Dihedral : 6.390 56.547 3662 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.64 % Allowed : 18.83 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3136 helix: 0.91 (0.15), residues: 1232 sheet: 0.42 (0.24), residues: 400 loop : -1.26 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 109 TYR 0.014 0.002 TYR B 95 PHE 0.013 0.002 PHE A 122 TRP 0.006 0.001 TRP F 79 HIS 0.019 0.002 HIS F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (24872) covalent geometry : angle 0.61616 / 0.33 (33752) SS BOND : bond 0.00472 / 0.28 ( 8) SS BOND : angle 1.64028 / 1.02 ( 16) hydrogen bonds : bond 0.06148 / 4.27 ( 1034) hydrogen bonds : angle 4.47005 / 3.28 ( 2853) metal coordination : bond 0.23771 / 17.35 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 227 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7889 (mt0) cc_final: 0.7363 (tp40) REVERT: A 131 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6578 (pp20) REVERT: A 172 GLU cc_start: 0.7532 (tt0) cc_final: 0.7049 (tm-30) REVERT: A 259 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7768 (ttmp) REVERT: A 315 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7038 (mtp-110) REVERT: B 53 GLN cc_start: 0.7920 (mt0) cc_final: 0.7318 (mm110) REVERT: B 131 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6631 (pp20) REVERT: B 172 GLU cc_start: 0.7814 (tp30) cc_final: 0.6897 (tm-30) REVERT: B 259 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7774 (ttmp) REVERT: B 312 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7279 (tp30) REVERT: B 315 ARG cc_start: 0.7384 (ttt90) cc_final: 0.7017 (mtp-110) REVERT: C 53 GLN cc_start: 0.7894 (mt0) cc_final: 0.7357 (tp40) REVERT: C 66 ARG cc_start: 0.5962 (OUTLIER) cc_final: 0.5003 (ttm170) REVERT: C 131 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6613 (pp20) REVERT: C 172 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: C 259 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7777 (ttmp) REVERT: C 315 ARG cc_start: 0.7409 (ttt90) cc_final: 0.7009 (mtp-110) REVERT: C 385 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6885 (p0) REVERT: D 53 GLN cc_start: 0.7936 (mt0) cc_final: 0.7363 (tp40) REVERT: D 131 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: D 259 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7793 (ttmp) REVERT: D 315 ARG cc_start: 0.7409 (ttt90) cc_final: 0.6985 (mtp-110) REVERT: D 385 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6880 (p0) REVERT: E 93 GLN cc_start: 0.7576 (mp10) cc_final: 0.6952 (mm-40) REVERT: E 173 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5975 (ttm170) REVERT: E 283 MET cc_start: 0.8801 (mtp) cc_final: 0.8554 (mtp) REVERT: E 338 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7175 (mtt180) REVERT: F 93 GLN cc_start: 0.7540 (mp10) cc_final: 0.6922 (mm-40) REVERT: F 173 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5915 (ttm170) REVERT: F 283 MET cc_start: 0.8808 (mtp) cc_final: 0.8554 (mtp) REVERT: F 338 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7245 (mtt180) REVERT: F 385 ASP cc_start: 0.8330 (p0) cc_final: 0.8120 (p0) REVERT: G 93 GLN cc_start: 0.7531 (mp10) cc_final: 0.6900 (mm-40) REVERT: G 173 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5928 (ttm170) REVERT: G 283 MET cc_start: 0.8824 (mtp) cc_final: 0.8578 (mtp) REVERT: G 338 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7220 (mtt180) REVERT: G 385 ASP cc_start: 0.8333 (p0) cc_final: 0.8128 (p0) REVERT: H 88 GLU cc_start: 0.7660 (pt0) cc_final: 0.7423 (pt0) REVERT: H 93 GLN cc_start: 0.7572 (mp10) cc_final: 0.6969 (mm-40) REVERT: H 173 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5963 (ttm170) REVERT: H 338 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7244 (mtt180) REVERT: H 385 ASP cc_start: 0.8331 (p0) cc_final: 0.8124 (p0) outliers start: 112 outliers final: 42 residues processed: 318 average time/residue: 0.7817 time to fit residues: 281.2352 Evaluate side-chains 288 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 268 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 279 optimal weight: 0.0770 chunk 175 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122484 restraints weight = 25247.014| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.77 r_work: 0.3380 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24912 Z= 0.204 Angle : 0.576 8.311 33768 Z= 0.304 Chirality : 0.048 0.231 3688 Planarity : 0.005 0.051 4496 Dihedral : 6.471 58.393 3662 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.09 % Allowed : 17.76 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3136 helix: 0.91 (0.15), residues: 1232 sheet: 0.13 (0.24), residues: 408 loop : -1.16 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 109 TYR 0.013 0.002 TYR A 95 PHE 0.012 0.002 PHE A 31 TRP 0.006 0.001 TRP E 79 HIS 0.026 0.002 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (24872) covalent geometry : angle 0.57548 / 0.30 (33752) SS BOND : bond 0.00360 / 0.21 ( 8) SS BOND : angle 1.29224 / 0.79 ( 16) hydrogen bonds : bond 0.05604 / 3.89 ( 1034) hydrogen bonds : angle 4.32339 / 3.17 ( 2853) metal coordination : bond 0.02922 / 2.20 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 219 time to evaluate : 0.912 Fit side-chains REVERT: A 53 GLN cc_start: 0.7857 (mt0) cc_final: 0.7270 (mm110) REVERT: A 131 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6708 (pp20) REVERT: A 172 GLU cc_start: 0.7478 (tt0) cc_final: 0.7004 (tm-30) REVERT: A 259 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7766 (ttmp) REVERT: A 315 ARG cc_start: 0.7408 (ttt90) cc_final: 0.6985 (mtp-110) REVERT: B 53 GLN cc_start: 0.7905 (mt0) cc_final: 0.7300 (mm110) REVERT: B 172 GLU cc_start: 0.7751 (tp30) cc_final: 0.6844 (OUTLIER) REVERT: B 259 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7825 (ttmp) REVERT: B 312 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7257 (tp30) REVERT: B 315 ARG cc_start: 0.7427 (ttt90) cc_final: 0.6990 (mtp-110) REVERT: C 53 GLN cc_start: 0.7876 (mt0) cc_final: 0.7347 (mm-40) REVERT: C 66 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.4990 (ttm170) REVERT: C 172 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: C 259 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7769 (ttmp) REVERT: C 385 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6940 (p0) REVERT: D 53 GLN cc_start: 0.7869 (mt0) cc_final: 0.7344 (mm-40) REVERT: D 259 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7760 (ttmp) REVERT: D 303 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7472 (tppt) REVERT: D 315 ARG cc_start: 0.7344 (ttt90) cc_final: 0.6926 (mtp-110) REVERT: D 385 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6942 (p0) REVERT: E 31 PHE cc_start: 0.7718 (t80) cc_final: 0.7413 (t80) REVERT: E 93 GLN cc_start: 0.7688 (mp10) cc_final: 0.7026 (mm-40) REVERT: E 283 MET cc_start: 0.8782 (mtp) cc_final: 0.8491 (mtp) REVERT: E 338 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7212 (mtt180) REVERT: F 283 MET cc_start: 0.8800 (mtp) cc_final: 0.8500 (mtp) REVERT: F 338 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7208 (mtt180) REVERT: G 31 PHE cc_start: 0.7717 (t80) cc_final: 0.7414 (t80) REVERT: G 93 GLN cc_start: 0.7637 (mp10) cc_final: 0.6985 (mm-40) REVERT: G 283 MET cc_start: 0.8804 (mtp) cc_final: 0.8520 (mtp) REVERT: G 338 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7207 (mtt180) REVERT: H 31 PHE cc_start: 0.7639 (t80) cc_final: 0.7323 (t80) REVERT: H 88 GLU cc_start: 0.7571 (pt0) cc_final: 0.7361 (pt0) REVERT: H 173 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.5940 (ttm170) REVERT: H 338 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7245 (mtt180) outliers start: 123 outliers final: 58 residues processed: 316 average time/residue: 0.7592 time to fit residues: 270.7375 Evaluate side-chains 281 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 10.0000 chunk 13 optimal weight: 0.0570 chunk 301 optimal weight: 0.0370 chunk 257 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS E 377 HIS F 251 HIS F 271 HIS F 345 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS G 271 HIS G 345 GLN G 377 HIS H 251 HIS H 271 HIS H 377 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125274 restraints weight = 24913.108| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.85 r_work: 0.3416 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.955 24912 Z= 0.492 Angle : 0.500 7.492 33768 Z= 0.259 Chirality : 0.045 0.222 3688 Planarity : 0.004 0.049 4496 Dihedral : 5.938 59.985 3662 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.18 % Allowed : 18.63 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3136 helix: 1.25 (0.15), residues: 1224 sheet: 0.18 (0.24), residues: 408 loop : -1.07 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 137 TYR 0.009 0.001 TYR A 95 PHE 0.010 0.001 PHE D 31 TRP 0.007 0.001 TRP G 79 HIS 0.020 0.001 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24872) covalent geometry : angle 0.49996 / 0.26 (33752) SS BOND : bond 0.00292 / 0.16 ( 8) SS BOND : angle 0.99699 / 0.58 ( 16) hydrogen bonds : bond 0.04289 / 2.96 ( 1034) hydrogen bonds : angle 4.00688 / 2.95 ( 2853) metal coordination : bond 0.39879 / 30.16 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 230 time to evaluate : 1.160 Fit side-chains REVERT: A 32 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7649 (t0) REVERT: A 53 GLN cc_start: 0.7783 (mt0) cc_final: 0.7227 (mm110) REVERT: A 66 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.4601 (ttm170) REVERT: A 172 GLU cc_start: 0.7476 (tt0) cc_final: 0.7028 (tm-30) REVERT: A 385 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6966 (p0) REVERT: B 53 GLN cc_start: 0.7837 (mt0) cc_final: 0.7281 (mm-40) REVERT: B 66 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.4696 (ttm170) REVERT: B 172 GLU cc_start: 0.7795 (tp30) cc_final: 0.6892 (tm-30) REVERT: B 312 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7304 (tp30) REVERT: B 315 ARG cc_start: 0.7414 (ttt90) cc_final: 0.7024 (mtp-110) REVERT: C 32 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7757 (t0) REVERT: C 53 GLN cc_start: 0.7832 (mt0) cc_final: 0.7256 (mm110) REVERT: C 172 GLU cc_start: 0.7562 (tt0) cc_final: 0.7177 (tm-30) REVERT: D 53 GLN cc_start: 0.7747 (mt0) cc_final: 0.7177 (mm110) REVERT: D 66 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4669 (ttm170) REVERT: E 31 PHE cc_start: 0.7615 (t80) cc_final: 0.7330 (t80) REVERT: E 173 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6017 (ttm170) REVERT: E 281 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7176 (ttm110) REVERT: E 283 MET cc_start: 0.8771 (mtp) cc_final: 0.8551 (mtp) REVERT: E 338 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7202 (mtt180) REVERT: F 31 PHE cc_start: 0.7598 (t80) cc_final: 0.7359 (t80) REVERT: F 88 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: F 173 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.5931 (ttm170) REVERT: F 283 MET cc_start: 0.8758 (mtp) cc_final: 0.8533 (mtp) REVERT: F 338 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7257 (mtt180) REVERT: G 31 PHE cc_start: 0.7612 (t80) cc_final: 0.7380 (t80) REVERT: G 173 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6011 (ttm170) REVERT: G 338 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7210 (mtt180) REVERT: H 31 PHE cc_start: 0.7613 (t80) cc_final: 0.7357 (t80) REVERT: H 338 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7136 (mtt180) outliers start: 101 outliers final: 53 residues processed: 314 average time/residue: 0.6906 time to fit residues: 247.3593 Evaluate side-chains 283 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 259 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 216 optimal weight: 0.0770 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 404 ASN C 404 ASN D 404 ASN E 271 HIS E 335 ASN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125952 restraints weight = 23985.292| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.69 r_work: 0.3421 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.910 24912 Z= 0.229 Angle : 0.506 7.369 33768 Z= 0.262 Chirality : 0.045 0.220 3688 Planarity : 0.004 0.050 4496 Dihedral : 5.794 59.844 3662 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.56 % Allowed : 19.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3136 helix: 1.33 (0.15), residues: 1224 sheet: 0.17 (0.24), residues: 408 loop : -1.01 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 109 TYR 0.009 0.001 TYR E 333 PHE 0.010 0.001 PHE A 31 TRP 0.005 0.001 TRP G 79 HIS 0.026 0.002 HIS H 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24872) covalent geometry : angle 0.50538 / 0.26 (33752) SS BOND : bond 0.00275 / 0.16 ( 8) SS BOND : angle 0.91367 / 0.54 ( 16) hydrogen bonds : bond 0.04282 / 2.96 ( 1034) hydrogen bonds : angle 3.95057 / 2.91 ( 2853) metal coordination : bond 0.16206 / 10.97 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 225 time to evaluate : 0.893 Fit side-chains REVERT: A 53 GLN cc_start: 0.7745 (mt0) cc_final: 0.7176 (mm110) REVERT: A 66 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.4791 (ttm170) REVERT: A 131 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: A 172 GLU cc_start: 0.7453 (tt0) cc_final: 0.6999 (tm-30) REVERT: B 53 GLN cc_start: 0.7783 (mt0) cc_final: 0.7200 (mm110) REVERT: B 131 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: B 172 GLU cc_start: 0.7773 (tp30) cc_final: 0.6879 (tm-30) REVERT: B 312 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7277 (tp30) REVERT: B 315 ARG cc_start: 0.7425 (ttt90) cc_final: 0.6955 (mtp-110) REVERT: C 53 GLN cc_start: 0.7807 (mt0) cc_final: 0.7240 (mm110) REVERT: C 131 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: C 172 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: D 53 GLN cc_start: 0.7650 (mt0) cc_final: 0.7108 (mm110) REVERT: D 66 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.4796 (ttm170) REVERT: D 131 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6693 (pp20) REVERT: E 31 PHE cc_start: 0.7593 (t80) cc_final: 0.7368 (t80) REVERT: E 173 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6009 (ttm170) REVERT: E 281 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7162 (ttm110) REVERT: E 283 MET cc_start: 0.8767 (mtp) cc_final: 0.8529 (mtp) REVERT: E 338 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7173 (mtt180) REVERT: F 31 PHE cc_start: 0.7550 (t80) cc_final: 0.7297 (t80) REVERT: F 88 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: F 173 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.5829 (ttm170) REVERT: F 283 MET cc_start: 0.8770 (mtp) cc_final: 0.8527 (mtp) REVERT: F 338 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7214 (mtt180) REVERT: G 31 PHE cc_start: 0.7626 (t80) cc_final: 0.7385 (t80) REVERT: G 173 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5971 (ttm170) REVERT: G 283 MET cc_start: 0.8759 (mtp) cc_final: 0.8530 (mtp) REVERT: G 338 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: H 173 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6067 (ttm170) REVERT: H 338 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7205 (mtt180) outliers start: 86 outliers final: 54 residues processed: 298 average time/residue: 0.6879 time to fit residues: 233.1114 Evaluate side-chains 285 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 271 HIS E 335 ASN F 335 ASN G 335 ASN H 335 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124430 restraints weight = 24494.849| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.64 r_work: 0.3403 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.765 24912 Z= 0.220 Angle : 0.532 7.745 33768 Z= 0.276 Chirality : 0.046 0.220 3688 Planarity : 0.004 0.052 4496 Dihedral : 6.116 59.625 3662 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.18 % Allowed : 18.75 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3136 helix: 1.23 (0.15), residues: 1232 sheet: 0.13 (0.25), residues: 368 loop : -1.03 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 137 TYR 0.011 0.001 TYR B 95 PHE 0.011 0.001 PHE A 31 TRP 0.005 0.001 TRP H 79 HIS 0.018 0.001 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24872) covalent geometry : angle 0.53165 / 0.28 (33752) SS BOND : bond 0.00314 / 0.18 ( 8) SS BOND : angle 0.96127 / 0.59 ( 16) hydrogen bonds : bond 0.04772 / 3.31 ( 1034) hydrogen bonds : angle 4.02952 / 2.97 ( 2853) metal coordination : bond 0.13576 / 9.18 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 224 time to evaluate : 1.007 Fit side-chains REVERT: A 39 LYS cc_start: 0.6815 (mttm) cc_final: 0.6400 (mttm) REVERT: A 53 GLN cc_start: 0.7694 (mt0) cc_final: 0.7161 (mm110) REVERT: A 172 GLU cc_start: 0.7450 (tt0) cc_final: 0.6992 (tm-30) REVERT: A 259 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7786 (ttmp) REVERT: B 53 GLN cc_start: 0.7810 (mt0) cc_final: 0.7264 (mm-40) REVERT: B 66 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.4797 (ttm170) REVERT: B 131 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6718 (pp20) REVERT: B 172 GLU cc_start: 0.7759 (tp30) cc_final: 0.6869 (tm-30) REVERT: B 259 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7892 (ttmp) REVERT: B 312 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7327 (tp30) REVERT: B 315 ARG cc_start: 0.7416 (ttt90) cc_final: 0.6983 (mtp-110) REVERT: C 53 GLN cc_start: 0.7746 (mt0) cc_final: 0.7155 (mm110) REVERT: C 66 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5012 (ttm170) REVERT: C 131 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6739 (pp20) REVERT: C 172 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: C 259 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7795 (ttmp) REVERT: D 53 GLN cc_start: 0.7652 (mt0) cc_final: 0.7111 (mm110) REVERT: D 131 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: D 259 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7890 (ttmp) REVERT: E 88 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: E 173 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5867 (ttm170) REVERT: E 281 ARG cc_start: 0.7787 (ttp-110) cc_final: 0.7196 (ttm110) REVERT: E 283 MET cc_start: 0.8782 (mtp) cc_final: 0.8537 (mtp) REVERT: E 338 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7176 (mtt180) REVERT: F 88 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7471 (pt0) REVERT: F 173 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5831 (ttm170) REVERT: F 283 MET cc_start: 0.8780 (mtp) cc_final: 0.8528 (mtp) REVERT: F 303 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7354 (mmtt) REVERT: F 338 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7183 (mtt180) REVERT: G 173 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.5841 (ttm170) REVERT: G 283 MET cc_start: 0.8766 (mtp) cc_final: 0.8537 (mtp) REVERT: G 303 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7330 (mmtt) REVERT: G 338 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7146 (mtt180) REVERT: H 173 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.5916 (ttm170) REVERT: H 338 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7155 (mtt180) outliers start: 101 outliers final: 58 residues processed: 305 average time/residue: 0.7510 time to fit residues: 258.4851 Evaluate side-chains 296 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 216 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 276 optimal weight: 0.5980 chunk 311 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 271 HIS E 335 ASN F 335 ASN G 53 GLN G 335 ASN H 335 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.147521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123069 restraints weight = 23964.220| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.68 r_work: 0.3387 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.922 24912 Z= 0.276 Angle : 0.574 8.042 33768 Z= 0.300 Chirality : 0.048 0.224 3688 Planarity : 0.005 0.054 4496 Dihedral : 6.357 59.457 3662 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.30 % Allowed : 18.67 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3136 helix: 1.08 (0.15), residues: 1232 sheet: 0.02 (0.26), residues: 360 loop : -1.10 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 137 TYR 0.012 0.002 TYR B 95 PHE 0.014 0.002 PHE D 31 TRP 0.004 0.001 TRP E 79 HIS 0.010 0.001 HIS G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (24872) covalent geometry : angle 0.57414 / 0.30 (33752) SS BOND : bond 0.00360 / 0.21 ( 8) SS BOND : angle 1.08710 / 0.67 ( 16) hydrogen bonds : bond 0.05488 / 3.81 ( 1034) hydrogen bonds : angle 4.19440 / 3.08 ( 2853) metal coordination : bond 0.16344 / 11.05 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 226 time to evaluate : 0.837 Fit side-chains REVERT: A 39 LYS cc_start: 0.6832 (mttm) cc_final: 0.6405 (mttm) REVERT: A 53 GLN cc_start: 0.7707 (mt0) cc_final: 0.7160 (mm110) REVERT: A 66 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.4909 (ttm170) REVERT: A 131 GLU cc_start: 0.6806 (pp20) cc_final: 0.6320 (pp20) REVERT: A 172 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: A 259 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7810 (ttmp) REVERT: B 39 LYS cc_start: 0.6916 (mttm) cc_final: 0.6476 (mttp) REVERT: B 53 GLN cc_start: 0.7805 (mt0) cc_final: 0.7220 (mm110) REVERT: B 66 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.4842 (ttm170) REVERT: B 131 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6818 (pp20) REVERT: B 172 GLU cc_start: 0.7804 (tp30) cc_final: 0.6916 (OUTLIER) REVERT: B 259 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7832 (ttmp) REVERT: B 312 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7426 (tp30) REVERT: B 315 ARG cc_start: 0.7433 (ttt90) cc_final: 0.6998 (mtp-110) REVERT: C 53 GLN cc_start: 0.7731 (mt0) cc_final: 0.7192 (mm110) REVERT: C 131 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: C 172 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: C 259 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7843 (ttmp) REVERT: D 39 LYS cc_start: 0.6937 (mttm) cc_final: 0.6485 (mttp) REVERT: D 53 GLN cc_start: 0.7675 (mt0) cc_final: 0.7174 (mm110) REVERT: D 66 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.4931 (ttm170) REVERT: D 131 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: D 259 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7829 (ttmp) REVERT: E 88 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: E 173 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5823 (ttm170) REVERT: E 281 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7258 (ttm110) REVERT: E 283 MET cc_start: 0.8796 (mtp) cc_final: 0.8549 (mtp) REVERT: E 338 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: F 88 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: F 173 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.5870 (ttm170) REVERT: F 283 MET cc_start: 0.8809 (mtp) cc_final: 0.8557 (mtp) REVERT: F 303 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7422 (mmtt) REVERT: F 338 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7217 (mtt180) REVERT: G 173 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5801 (ttm170) REVERT: G 283 MET cc_start: 0.8797 (mtp) cc_final: 0.8566 (mtp) REVERT: G 303 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7398 (mmtt) REVERT: G 338 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7194 (mtt180) REVERT: H 173 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5957 (ttm170) REVERT: H 303 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7438 (mmtt) REVERT: H 338 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7182 (mtt180) outliers start: 104 outliers final: 58 residues processed: 310 average time/residue: 0.7145 time to fit residues: 251.1483 Evaluate side-chains 297 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 215 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 293 optimal weight: 0.8980 chunk 303 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 chunk 200 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 271 HIS E 335 ASN F 53 GLN F 335 ASN F 377 HIS ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN H 53 GLN H 335 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127539 restraints weight = 23969.869| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.62 r_work: 0.3451 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.749 24912 Z= 0.184 Angle : 0.484 6.813 33768 Z= 0.247 Chirality : 0.044 0.217 3688 Planarity : 0.004 0.047 4496 Dihedral : 5.830 59.278 3662 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.52 % Allowed : 20.65 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3136 helix: 1.45 (0.15), residues: 1224 sheet: 0.15 (0.25), residues: 368 loop : -0.96 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 137 TYR 0.009 0.001 TYR A 333 PHE 0.011 0.001 PHE A 31 TRP 0.006 0.001 TRP E 79 HIS 0.012 0.001 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (24872) covalent geometry : angle 0.48409 / 0.25 (33752) SS BOND : bond 0.00279 / 0.16 ( 8) SS BOND : angle 0.81328 / 0.48 ( 16) hydrogen bonds : bond 0.03551 / 2.45 ( 1034) hydrogen bonds : angle 3.78821 / 2.79 ( 2853) metal coordination : bond 0.13257 / 8.96 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 232 time to evaluate : 1.000 Fit side-chains REVERT: A 39 LYS cc_start: 0.6825 (mttm) cc_final: 0.6516 (mttm) REVERT: A 53 GLN cc_start: 0.7634 (mt0) cc_final: 0.7108 (mm110) REVERT: A 172 GLU cc_start: 0.7455 (tt0) cc_final: 0.7029 (tm-30) REVERT: A 259 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7816 (ttmp) REVERT: B 39 LYS cc_start: 0.6918 (mttm) cc_final: 0.6590 (mttm) REVERT: B 53 GLN cc_start: 0.7652 (mt0) cc_final: 0.7151 (mm-40) REVERT: B 172 GLU cc_start: 0.7755 (tp30) cc_final: 0.6894 (tm-30) REVERT: B 312 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7365 (tp30) REVERT: C 39 LYS cc_start: 0.6836 (mttm) cc_final: 0.6389 (mttp) REVERT: C 53 GLN cc_start: 0.7640 (mt0) cc_final: 0.7137 (mm110) REVERT: C 172 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7183 (tm-30) REVERT: D 39 LYS cc_start: 0.6943 (mttm) cc_final: 0.6620 (mttm) REVERT: D 53 GLN cc_start: 0.7607 (mt0) cc_final: 0.7080 (mm110) REVERT: E 88 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: E 119 MET cc_start: 0.8658 (mmt) cc_final: 0.8097 (mmt) REVERT: E 173 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6005 (ttm170) REVERT: E 281 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7165 (ttm110) REVERT: E 283 MET cc_start: 0.8770 (mtp) cc_final: 0.8488 (mtp) REVERT: F 173 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.5869 (ttm170) REVERT: F 283 MET cc_start: 0.8781 (mtp) cc_final: 0.8497 (mtp) REVERT: G 173 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.5917 (ttm170) REVERT: G 283 MET cc_start: 0.8754 (mtp) cc_final: 0.8489 (mtp) REVERT: H 173 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.5959 (ttm170) outliers start: 61 outliers final: 37 residues processed: 280 average time/residue: 0.7202 time to fit residues: 230.2003 Evaluate side-chains 268 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 146 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 11 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.0470 chunk 154 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 271 HIS E 345 GLN E 410 ASN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 ASN F 410 ASN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 410 ASN H 345 GLN H 410 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129597 restraints weight = 23447.896| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.56 r_work: 0.3479 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.888 24912 Z= 0.205 Angle : 0.465 6.143 33768 Z= 0.237 Chirality : 0.043 0.219 3688 Planarity : 0.004 0.048 4496 Dihedral : 5.260 59.145 3662 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.95 % Allowed : 21.65 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3136 helix: 1.60 (0.15), residues: 1232 sheet: 0.27 (0.26), residues: 328 loop : -0.74 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 137 TYR 0.009 0.001 TYR F 333 PHE 0.012 0.001 PHE A 31 TRP 0.006 0.000 TRP G 79 HIS 0.012 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (24872) covalent geometry : angle 0.46522 / 0.24 (33752) SS BOND : bond 0.00218 / 0.13 ( 8) SS BOND : angle 0.70419 / 0.40 ( 16) hydrogen bonds : bond 0.03201 / 2.20 ( 1034) hydrogen bonds : angle 3.60730 / 2.66 ( 2853) metal coordination : bond 0.15704 / 10.61 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.968 Fit side-chains REVERT: A 39 LYS cc_start: 0.6878 (mttm) cc_final: 0.6531 (mttm) REVERT: A 53 GLN cc_start: 0.7627 (mt0) cc_final: 0.7091 (mm110) REVERT: A 172 GLU cc_start: 0.7415 (tt0) cc_final: 0.6991 (tm-30) REVERT: B 39 LYS cc_start: 0.6996 (mttm) cc_final: 0.6604 (mttm) REVERT: B 53 GLN cc_start: 0.7653 (mt0) cc_final: 0.7123 (mm110) REVERT: B 172 GLU cc_start: 0.7851 (tp30) cc_final: 0.6992 (tm-30) REVERT: B 312 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7216 (tp30) REVERT: B 315 ARG cc_start: 0.7392 (ttt90) cc_final: 0.6886 (mtp-110) REVERT: C 39 LYS cc_start: 0.6920 (mttm) cc_final: 0.6419 (mttp) REVERT: C 53 GLN cc_start: 0.7625 (mt0) cc_final: 0.7099 (mm110) REVERT: C 172 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: D 39 LYS cc_start: 0.7043 (mttm) cc_final: 0.6651 (mttm) REVERT: D 53 GLN cc_start: 0.7628 (mt0) cc_final: 0.7112 (mm110) REVERT: E 173 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5928 (ttm170) REVERT: E 281 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7125 (ttm110) REVERT: E 283 MET cc_start: 0.8758 (mtp) cc_final: 0.8479 (mtp) REVERT: F 88 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: F 173 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5844 (ttm170) REVERT: F 283 MET cc_start: 0.8774 (mtp) cc_final: 0.8490 (mtp) REVERT: G 173 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5882 (ttm170) REVERT: H 173 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.5952 (ttm170) outliers start: 47 outliers final: 32 residues processed: 277 average time/residue: 0.6720 time to fit residues: 212.6858 Evaluate side-chains 259 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124397 restraints weight = 23961.089| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.62 r_work: 0.3406 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.707 24912 Z= 0.221 Angle : 0.545 7.443 33768 Z= 0.283 Chirality : 0.047 0.219 3688 Planarity : 0.004 0.053 4496 Dihedral : 6.148 59.950 3662 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.11 % Allowed : 21.85 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3136 helix: 1.38 (0.15), residues: 1232 sheet: 0.16 (0.25), residues: 368 loop : -0.93 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 137 TYR 0.012 0.001 TYR H 333 PHE 0.013 0.002 PHE B 31 TRP 0.004 0.001 TRP E 79 HIS 0.014 0.001 HIS E 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (24872) covalent geometry : angle 0.54474 / 0.28 (33752) SS BOND : bond 0.00332 / 0.19 ( 8) SS BOND : angle 0.94754 / 0.58 ( 16) hydrogen bonds : bond 0.04912 / 3.40 ( 1034) hydrogen bonds : angle 3.98876 / 2.94 ( 2853) metal coordination : bond 0.12566 / 8.51 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8405.05 seconds wall clock time: 143 minutes 47.02 seconds (8627.02 seconds total)