Starting phenix.real_space_refine on Fri May 23 18:19:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_36060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_36060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_36060.map" model { file = "/net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_36060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j85_36060/05_2025/8j85_36060.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.63, per 1000 atoms: 0.81 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: 6.76 Conformation dependent library (CDL) restraints added in 4.6 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: 2.87 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: 8.77 Time building geometry restraints manager: 9.21 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 - 17.95: 12714 17.95 - 35.90: 1513 35.90 - 53.84: 418 53.84 - 71.79: 117 71.79 - 89.74: 54 Dihedral angle restraints: 14816 sinusoidal: 5856 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 14813 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: 8.710 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: 0.000 Extract box with map and model: 0.880 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 69.530 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 17.827 89.739 9112 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP E 79 HIS 0.007 0.001 HIS H 251 PHE 0.011 0.001 PHE F 299 TYR 0.009 0.001 TYR E 333 ARG 0.002 0.000 ARG G 199 Details of bonding type rmsd hydrogen bonds : bond 0.15791 ( 1034) hydrogen bonds : angle 6.45987 ( 2853) metal coordination : bond 0.02663 ( 32) SS BOND : bond 0.01736 ( 8) SS BOND : angle 1.89642 ( 16) covalent geometry : bond 0.00643 (24872) covalent geometry : angle 0.74903 (33752) *********************** 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 : 2.697 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: 1.8537 time to fit residues: 1013.9400 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 : 2.775 ------------------------------------------------------------------------------- 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 263 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.151122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126475 restraints weight = 25366.911| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.66 r_work: 0.3439 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2177 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= 0.138 Angle : 0.530 7.261 33768 Z= 0.279 Chirality : 0.046 0.240 3688 Planarity : 0.005 0.046 4496 Dihedral : 9.375 89.978 3767 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.07 % Allowed : 21.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3136 helix: 1.12 (0.15), residues: 1232 sheet: 0.57 (0.25), residues: 400 loop : -1.26 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 79 HIS 0.007 0.001 HIS A 251 PHE 0.009 0.001 PHE F 294 TYR 0.011 0.001 TYR C 95 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1034) hydrogen bonds : angle 4.36536 ( 2853) metal coordination : bond 0.00439 ( 32) SS BOND : bond 0.00181 ( 8) SS BOND : angle 1.39053 ( 16) covalent geometry : bond 0.00315 (24872) covalent geometry : angle 0.52905 (33752) *********************** 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 313 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 2.461 Fit side-chains REVERT: A 315 ARG cc_start: 0.7329 (ttt90) cc_final: 0.6934 (mtp-110) REVERT: B 172 GLU cc_start: 0.7856 (tp30) cc_final: 0.6914 (tm-30) REVERT: B 312 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7086 (tp30) REVERT: B 315 ARG cc_start: 0.7310 (ttt90) cc_final: 0.6934 (mtp-110) REVERT: C 31 PHE cc_start: 0.8299 (t80) cc_final: 0.7894 (t80) REVERT: C 315 ARG cc_start: 0.7330 (ttt90) cc_final: 0.6913 (mtp-110) REVERT: D 172 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: D 315 ARG cc_start: 0.7241 (ttt90) cc_final: 0.6864 (mtp-110) REVERT: E 93 GLN cc_start: 0.7448 (mp10) cc_final: 0.6954 (mm-40) REVERT: E 173 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6018 (ttm170) REVERT: E 283 MET cc_start: 0.8776 (mtp) cc_final: 0.8487 (mtp) REVERT: E 338 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7250 (mtt180) REVERT: E 385 ASP cc_start: 0.8147 (p0) cc_final: 0.7878 (p0) REVERT: F 93 GLN cc_start: 0.7433 (mp10) cc_final: 0.6952 (mm-40) REVERT: F 173 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6112 (ttm170) REVERT: F 283 MET cc_start: 0.8781 (mtp) cc_final: 0.8475 (mtp) REVERT: F 338 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7237 (mtt180) REVERT: F 385 ASP cc_start: 0.8125 (p0) cc_final: 0.7864 (p0) REVERT: G 93 GLN cc_start: 0.7398 (mp10) cc_final: 0.6871 (mm-40) REVERT: G 173 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.5991 (ttm170) REVERT: G 283 MET cc_start: 0.8792 (mtp) cc_final: 0.8500 (mtp) REVERT: G 338 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7324 (mtt180) REVERT: G 385 ASP cc_start: 0.8082 (p0) cc_final: 0.7822 (p0) REVERT: H 88 GLU cc_start: 0.7522 (pt0) cc_final: 0.7313 (pt0) REVERT: H 93 GLN cc_start: 0.7411 (mp10) cc_final: 0.6903 (mm-40) REVERT: H 173 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6192 (ttm170) REVERT: H 338 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7266 (mtt180) REVERT: H 385 ASP cc_start: 0.8091 (p0) cc_final: 0.7853 (p0) outliers start: 50 outliers final: 18 residues processed: 299 average time/residue: 1.5792 time to fit residues: 534.2211 Evaluate side-chains 245 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 192 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 251 HIS F 271 HIS F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS G 271 HIS G 335 ASN H 251 HIS H 271 HIS H 335 ASN H 404 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127384 restraints weight = 24522.536| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.84 r_work: 0.3440 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.019 24912 Z= 0.538 Angle : 0.492 7.456 33768 Z= 0.256 Chirality : 0.045 0.223 3688 Planarity : 0.004 0.048 4496 Dihedral : 8.373 89.175 3758 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.94 % Allowed : 21.11 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3136 helix: 1.33 (0.15), residues: 1232 sheet: 0.74 (0.25), residues: 400 loop : -1.12 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.015 0.001 HIS E 251 PHE 0.008 0.001 PHE E 294 TYR 0.009 0.001 TYR A 333 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1034) hydrogen bonds : angle 4.05339 ( 2853) metal coordination : bond 0.44026 ( 32) SS BOND : bond 0.00336 ( 8) SS BOND : angle 1.17420 ( 16) covalent geometry : bond 0.00250 (24872) covalent geometry : angle 0.49105 (33752) *********************** 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 305 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7667 (mt0) cc_final: 0.7195 (mm110) REVERT: A 315 ARG cc_start: 0.7339 (ttt90) cc_final: 0.6952 (mtp-110) REVERT: B 53 GLN cc_start: 0.7688 (mt0) cc_final: 0.7208 (mm110) REVERT: B 172 GLU cc_start: 0.7905 (tp30) cc_final: 0.7010 (tm-30) REVERT: B 312 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7177 (tp30) REVERT: B 315 ARG cc_start: 0.7346 (ttt90) cc_final: 0.6935 (mtp-110) REVERT: C 53 GLN cc_start: 0.7681 (mt0) cc_final: 0.7175 (mm110) REVERT: C 172 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: C 315 ARG cc_start: 0.7353 (ttt90) cc_final: 0.6972 (mtp-110) REVERT: D 53 GLN cc_start: 0.7642 (mt0) cc_final: 0.7181 (tp40) REVERT: D 172 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: D 315 ARG cc_start: 0.7350 (ttt90) cc_final: 0.6885 (mtp-110) REVERT: E 173 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6017 (ttm170) REVERT: E 283 MET cc_start: 0.8749 (mtp) cc_final: 0.8510 (mtp) REVERT: E 338 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7313 (mtt180) REVERT: E 385 ASP cc_start: 0.8244 (p0) cc_final: 0.7996 (p0) REVERT: F 173 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6107 (ttm170) REVERT: F 283 MET cc_start: 0.8772 (mtp) cc_final: 0.8529 (mtp) REVERT: F 338 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7292 (mtt180) REVERT: F 385 ASP cc_start: 0.8226 (p0) cc_final: 0.8002 (p0) REVERT: G 173 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6030 (ttm170) REVERT: G 338 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7308 (mtt180) REVERT: G 385 ASP cc_start: 0.8199 (p0) cc_final: 0.7969 (p0) REVERT: H 173 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6175 (ttm170) REVERT: H 338 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7333 (mtt180) REVERT: H 385 ASP cc_start: 0.8224 (p0) cc_final: 0.7999 (p0) outliers start: 71 outliers final: 33 residues processed: 290 average time/residue: 1.5399 time to fit residues: 505.2200 Evaluate side-chains 264 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 2.569 ------------------------------------------------------------------------------- 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 B residue 76 LEU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 76 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 D residue 76 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 173 ARG 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 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 173 ARG Chi-restraints excluded: chain G residue 208 LEU 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 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 143 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 26 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124447 restraints weight = 24823.011| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.76 r_work: 0.3404 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24912 Z= 0.178 Angle : 0.560 8.156 33768 Z= 0.294 Chirality : 0.047 0.220 3688 Planarity : 0.005 0.054 4496 Dihedral : 8.322 84.165 3758 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.81 % Allowed : 19.99 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3136 helix: 1.19 (0.15), residues: 1232 sheet: 0.57 (0.25), residues: 400 loop : -1.09 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 79 HIS 0.027 0.002 HIS E 251 PHE 0.012 0.002 PHE F 294 TYR 0.012 0.002 TYR B 95 ARG 0.004 0.000 ARG G 109 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 1034) hydrogen bonds : angle 4.20768 ( 2853) metal coordination : bond 0.02443 ( 32) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.15444 ( 16) covalent geometry : bond 0.00417 (24872) covalent geometry : angle 0.55950 (33752) *********************** 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 319 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 227 time to evaluate : 2.845 Fit side-chains REVERT: A 53 GLN cc_start: 0.7835 (mt0) cc_final: 0.7325 (mm-40) REVERT: A 131 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6567 (pp20) REVERT: A 172 GLU cc_start: 0.7498 (tt0) cc_final: 0.7016 (tm-30) REVERT: A 259 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7804 (ttmp) REVERT: A 315 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6964 (mtp-110) REVERT: B 53 GLN cc_start: 0.7828 (mt0) cc_final: 0.7356 (mm-40) REVERT: B 131 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: B 172 GLU cc_start: 0.7881 (tp30) cc_final: 0.6940 (tm-30) REVERT: B 259 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7794 (ttmp) REVERT: B 312 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7300 (tp30) REVERT: B 315 ARG cc_start: 0.7343 (ttt90) cc_final: 0.6978 (mtp-110) REVERT: C 53 GLN cc_start: 0.7861 (mt0) cc_final: 0.7344 (tp40) REVERT: C 115 GLU cc_start: 0.8370 (tp30) cc_final: 0.8168 (tt0) REVERT: C 131 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: C 172 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: C 259 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7808 (ttmp) REVERT: C 315 ARG cc_start: 0.7306 (ttt90) cc_final: 0.6948 (mtp-110) REVERT: C 385 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6844 (p0) REVERT: D 53 GLN cc_start: 0.7843 (mt0) cc_final: 0.7334 (tp40) REVERT: D 115 GLU cc_start: 0.8367 (tp30) cc_final: 0.8166 (tt0) REVERT: D 131 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6574 (pp20) REVERT: D 259 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7817 (ttmp) REVERT: D 315 ARG cc_start: 0.7351 (ttt90) cc_final: 0.6941 (mtp-110) REVERT: D 385 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6886 (p0) REVERT: E 283 MET cc_start: 0.8776 (mtp) cc_final: 0.8519 (mtp) REVERT: E 338 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7159 (mtt180) REVERT: F 88 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7561 (pt0) REVERT: F 283 MET cc_start: 0.8796 (mtp) cc_final: 0.8552 (mtp) REVERT: F 338 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7166 (mtt180) REVERT: G 338 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7158 (mtt180) REVERT: H 338 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7188 (mtt180) outliers start: 92 outliers final: 44 residues processed: 301 average time/residue: 1.5148 time to fit residues: 515.9807 Evaluate side-chains 272 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 321 ILE Chi-restraints excluded: chain A residue 358 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 259 LYS Chi-restraints excluded: chain B residue 358 VAL 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 376 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 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 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 88 GLU 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 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 389 VAL Chi-restraints excluded: chain G residue 23 VAL 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 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 172 GLU 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 389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 217 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS G 271 HIS G 335 ASN H 271 HIS H 404 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121449 restraints weight = 25604.318| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.86 r_work: 0.3355 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.709 24912 Z= 0.423 Angle : 0.679 9.450 33768 Z= 0.360 Chirality : 0.053 0.215 3688 Planarity : 0.006 0.054 4496 Dihedral : 8.845 76.756 3758 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.38 % Allowed : 17.76 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3136 helix: 0.67 (0.14), residues: 1232 sheet: -0.04 (0.24), residues: 408 loop : -1.22 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 79 HIS 0.024 0.002 HIS E 251 PHE 0.015 0.002 PHE A 31 TYR 0.015 0.002 TYR A 95 ARG 0.003 0.001 ARG F 355 Details of bonding type rmsd hydrogen bonds : bond 0.06902 ( 1034) hydrogen bonds : angle 4.58642 ( 2853) metal coordination : bond 0.24900 ( 32) SS BOND : bond 0.00435 ( 8) SS BOND : angle 1.42259 ( 16) covalent geometry : bond 0.00729 (24872) covalent geometry : angle 0.67814 (33752) *********************** 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 340 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 210 time to evaluate : 2.679 Fit side-chains REVERT: A 53 GLN cc_start: 0.7843 (mt0) cc_final: 0.7302 (tp40) REVERT: A 131 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6753 (pp20) REVERT: A 172 GLU cc_start: 0.7479 (tt0) cc_final: 0.7020 (tm-30) REVERT: A 259 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7828 (ttmp) REVERT: A 303 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7494 (tppt) REVERT: A 315 ARG cc_start: 0.7514 (ttt90) cc_final: 0.7126 (mtp-110) REVERT: A 385 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7021 (p0) REVERT: B 53 GLN cc_start: 0.7860 (mt0) cc_final: 0.7293 (mm110) REVERT: B 131 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: B 172 GLU cc_start: 0.7779 (tp30) cc_final: 0.6884 (OUTLIER) REVERT: B 259 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7823 (ttmp) REVERT: B 303 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7452 (tppt) REVERT: B 312 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7326 (tp30) REVERT: B 315 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7063 (mtp-110) REVERT: B 385 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6995 (p0) REVERT: C 53 GLN cc_start: 0.7881 (mt0) cc_final: 0.7328 (tp40) REVERT: C 131 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6776 (pp20) REVERT: C 172 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7088 (tm-30) REVERT: C 259 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7831 (ttmp) REVERT: C 303 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7496 (tppt) REVERT: C 385 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6975 (p0) REVERT: D 53 GLN cc_start: 0.7915 (mt0) cc_final: 0.7344 (tp40) REVERT: D 131 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6775 (pp20) REVERT: D 259 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7832 (ttmp) REVERT: D 303 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7399 (tppt) REVERT: D 315 ARG cc_start: 0.7501 (ttt90) cc_final: 0.7082 (mtp-110) REVERT: D 385 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.7004 (p0) REVERT: E 31 PHE cc_start: 0.7634 (t80) cc_final: 0.7312 (t80) REVERT: E 119 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8359 (mmt) REVERT: E 173 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5759 (ttm170) REVERT: E 281 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7289 (ttm110) REVERT: E 283 MET cc_start: 0.8806 (mtp) cc_final: 0.8535 (mtp) REVERT: E 338 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7271 (mtt180) REVERT: F 88 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: F 119 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8361 (mmt) REVERT: F 173 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5814 (ttm170) REVERT: F 283 MET cc_start: 0.8823 (mtp) cc_final: 0.8535 (mtp) REVERT: F 338 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7290 (mtt180) REVERT: G 173 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5753 (ttm170) REVERT: G 338 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7284 (mtt180) REVERT: H 88 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: H 119 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8338 (mmt) REVERT: H 173 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5877 (ttm170) REVERT: H 338 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7283 (mtt180) outliers start: 130 outliers final: 56 residues processed: 309 average time/residue: 1.5756 time to fit residues: 549.3130 Evaluate side-chains 277 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 192 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 303 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 A residue 385 ASP 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 303 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 385 ASP 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 303 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 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 131 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 362 GLU 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 119 MET 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 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 119 MET 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 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 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 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 88 GLU Chi-restraints excluded: chain H residue 119 MET 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 389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 136 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 216 optimal weight: 0.5980 chunk 292 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN E 271 HIS E 345 GLN E 380 GLN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 HIS F 345 GLN F 380 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 HIS G 345 GLN G 380 GLN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 HIS H 345 GLN H 380 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126268 restraints weight = 24281.757| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.59 r_work: 0.3428 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.903 24912 Z= 0.395 Angle : 0.498 7.224 33768 Z= 0.257 Chirality : 0.045 0.222 3688 Planarity : 0.004 0.046 4496 Dihedral : 7.542 59.723 3758 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.48 % Allowed : 20.03 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3136 helix: 1.19 (0.15), residues: 1224 sheet: 0.08 (0.24), residues: 408 loop : -1.05 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 79 HIS 0.006 0.001 HIS D 251 PHE 0.009 0.001 PHE F 294 TYR 0.009 0.001 TYR F 333 ARG 0.001 0.000 ARG H 201 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1034) hydrogen bonds : angle 4.00027 ( 2853) metal coordination : bond 0.31893 ( 32) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.88933 ( 16) covalent geometry : bond 0.00233 (24872) covalent geometry : angle 0.49743 (33752) *********************** 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 313 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 229 time to evaluate : 2.647 Fit side-chains REVERT: A 53 GLN cc_start: 0.7765 (mt0) cc_final: 0.7206 (mm110) REVERT: A 131 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6694 (pp20) REVERT: A 172 GLU cc_start: 0.7447 (tt0) cc_final: 0.7034 (tm-30) REVERT: B 53 GLN cc_start: 0.7808 (mt0) cc_final: 0.7270 (mm-40) REVERT: B 172 GLU cc_start: 0.7779 (tp30) cc_final: 0.6884 (OUTLIER) REVERT: B 312 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7299 (tp30) REVERT: C 53 GLN cc_start: 0.7792 (mt0) cc_final: 0.7220 (mm-40) REVERT: C 115 GLU cc_start: 0.8198 (tp30) cc_final: 0.7798 (tp30) REVERT: C 172 GLU cc_start: 0.7584 (tt0) cc_final: 0.7211 (tm-30) REVERT: D 53 GLN cc_start: 0.7750 (mt0) cc_final: 0.7169 (mm110) REVERT: D 115 GLU cc_start: 0.8210 (tp30) cc_final: 0.7801 (tp30) REVERT: E 173 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.5954 (ttm170) REVERT: E 281 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7147 (ttm110) REVERT: E 283 MET cc_start: 0.8746 (mtp) cc_final: 0.8416 (mtp) REVERT: E 338 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7123 (mtt180) REVERT: F 88 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: F 173 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.5846 (ttm170) REVERT: F 283 MET cc_start: 0.8777 (mtp) cc_final: 0.8531 (mtp) REVERT: F 338 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: G 173 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.5947 (ttm170) REVERT: H 173 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5935 (ttm170) outliers start: 84 outliers final: 50 residues processed: 302 average time/residue: 1.4740 time to fit residues: 507.6778 Evaluate side-chains 271 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain C residue 96 SER 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 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 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 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 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 F residue 389 VAL Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 LEU 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 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 271 HIS E 335 ASN E 377 HIS F 271 HIS F 335 ASN F 377 HIS F 404 ASN G 271 HIS G 335 ASN G 377 HIS H 271 HIS H 335 ASN H 377 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128152 restraints weight = 24790.033| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.84 r_work: 0.3458 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.799 24912 Z= 0.346 Angle : 0.481 6.762 33768 Z= 0.245 Chirality : 0.044 0.222 3688 Planarity : 0.004 0.047 4496 Dihedral : 6.523 59.350 3758 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.90 % Allowed : 21.03 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3136 helix: 1.47 (0.15), residues: 1224 sheet: 0.31 (0.26), residues: 368 loop : -0.97 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.012 0.001 HIS E 251 PHE 0.010 0.001 PHE A 31 TYR 0.009 0.001 TYR F 333 ARG 0.002 0.000 ARG F 52 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1034) hydrogen bonds : angle 3.77457 ( 2853) metal coordination : bond 0.27997 ( 32) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.75940 ( 16) covalent geometry : bond 0.00195 (24872) covalent geometry : angle 0.48054 (33752) *********************** 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 298 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 2.315 Fit side-chains REVERT: A 53 GLN cc_start: 0.7713 (mt0) cc_final: 0.7150 (mm-40) REVERT: A 172 GLU cc_start: 0.7440 (tt0) cc_final: 0.7008 (tm-30) REVERT: B 53 GLN cc_start: 0.7769 (mt0) cc_final: 0.7189 (mm110) REVERT: B 172 GLU cc_start: 0.7775 (tp30) cc_final: 0.6894 (OUTLIER) REVERT: B 312 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7337 (tp30) REVERT: B 315 ARG cc_start: 0.7369 (ttt90) cc_final: 0.6941 (mtp-110) REVERT: C 53 GLN cc_start: 0.7749 (mt0) cc_final: 0.7185 (mm-40) REVERT: C 115 GLU cc_start: 0.8209 (tp30) cc_final: 0.7753 (tp30) REVERT: C 172 GLU cc_start: 0.7498 (tt0) cc_final: 0.7117 (tm-30) REVERT: D 53 GLN cc_start: 0.7646 (mt0) cc_final: 0.7077 (mm110) REVERT: D 115 GLU cc_start: 0.8210 (tp30) cc_final: 0.7757 (tp30) REVERT: E 173 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5947 (ttm170) REVERT: E 281 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7131 (ttm110) REVERT: E 283 MET cc_start: 0.8717 (mtp) cc_final: 0.8477 (mtp) REVERT: F 88 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: F 173 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5837 (ttm170) REVERT: F 283 MET cc_start: 0.8757 (mtp) cc_final: 0.8515 (mtp) REVERT: G 173 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.5915 (ttm170) REVERT: H 88 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: H 173 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6056 (ttm170) outliers start: 70 outliers final: 39 residues processed: 287 average time/residue: 1.6682 time to fit residues: 549.8635 Evaluate side-chains 270 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 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 96 SER 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 96 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 76 LEU 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 358 VAL Chi-restraints excluded: chain E residue 389 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 313 VAL Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 55 LEU 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 358 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 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 358 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 251 HIS E 271 HIS E 345 GLN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 HIS F 335 ASN G 271 HIS G 345 GLN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 HIS H 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123161 restraints weight = 24428.504| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.60 r_work: 0.3393 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.013 0.917 24912 Z= 0.446 Angle : 0.575 8.042 33768 Z= 0.300 Chirality : 0.048 0.223 3688 Planarity : 0.005 0.054 4496 Dihedral : 7.816 59.717 3758 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.60 % Allowed : 20.65 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3136 helix: 1.17 (0.15), residues: 1232 sheet: 0.14 (0.26), residues: 360 loop : -1.04 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.005 0.001 HIS E 253 PHE 0.013 0.002 PHE A 31 TYR 0.012 0.002 TYR G 333 ARG 0.002 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.05398 ( 1034) hydrogen bonds : angle 4.15859 ( 2853) metal coordination : bond 0.33607 ( 32) SS BOND : bond 0.00354 ( 8) SS BOND : angle 1.05397 ( 16) covalent geometry : bond 0.00466 (24872) covalent geometry : angle 0.57508 (33752) *********************** 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 310 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 2.630 Fit side-chains REVERT: A 53 GLN cc_start: 0.7718 (mt0) cc_final: 0.7175 (mm110) REVERT: A 66 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.4911 (ttm170) REVERT: A 131 GLU cc_start: 0.6783 (pp20) cc_final: 0.6262 (pp20) REVERT: A 172 GLU cc_start: 0.7477 (tt0) cc_final: 0.7018 (tm-30) REVERT: B 53 GLN cc_start: 0.7810 (mt0) cc_final: 0.7248 (mm110) REVERT: B 66 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.4875 (ttm170) REVERT: B 131 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6765 (pp20) REVERT: B 172 GLU cc_start: 0.7774 (tp30) cc_final: 0.6872 (OUTLIER) REVERT: B 312 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7435 (tp30) REVERT: B 315 ARG cc_start: 0.7402 (ttt90) cc_final: 0.6965 (mtp-110) REVERT: C 53 GLN cc_start: 0.7746 (mt0) cc_final: 0.7200 (mm110) REVERT: C 115 GLU cc_start: 0.8309 (tp30) cc_final: 0.7926 (tp30) REVERT: C 131 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6748 (pp20) REVERT: C 172 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: D 53 GLN cc_start: 0.7731 (mt0) cc_final: 0.7180 (mm110) REVERT: D 66 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.4944 (ttm170) REVERT: D 115 GLU cc_start: 0.8308 (tp30) cc_final: 0.7926 (tp30) REVERT: D 131 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: E 173 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.5864 (ttm170) REVERT: E 281 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7212 (ttm110) REVERT: E 283 MET cc_start: 0.8788 (mtp) cc_final: 0.8556 (mtp) REVERT: E 338 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7253 (mtt180) REVERT: F 88 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: F 173 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.5853 (ttm170) REVERT: F 283 MET cc_start: 0.8795 (mtp) cc_final: 0.8555 (mtp) REVERT: F 303 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7402 (mmtt) REVERT: F 338 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: G 173 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5828 (ttm170) REVERT: G 338 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7117 (mtt180) REVERT: H 88 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: H 173 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: H 303 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7431 (mmtt) REVERT: H 338 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7152 (mtt180) outliers start: 87 outliers final: 49 residues processed: 299 average time/residue: 1.5354 time to fit residues: 519.5390 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 : 2.439 ------------------------------------------------------------------------------- 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 251 HIS 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 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 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 172 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 389 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 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 389 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 GLU 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 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 226 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 255 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 271 HIS F 335 ASN G 271 HIS H 271 HIS H 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126621 restraints weight = 24851.505| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.83 r_work: 0.3438 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.787 24912 Z= 0.305 Angle : 0.501 7.161 33768 Z= 0.256 Chirality : 0.045 0.223 3688 Planarity : 0.004 0.046 4496 Dihedral : 7.027 59.663 3758 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.61 % Allowed : 21.44 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3136 helix: 1.42 (0.15), residues: 1224 sheet: 0.20 (0.25), residues: 368 loop : -0.95 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 79 HIS 0.007 0.001 HIS H 251 PHE 0.011 0.001 PHE A 31 TYR 0.009 0.001 TYR A 333 ARG 0.001 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1034) hydrogen bonds : angle 3.86651 ( 2853) metal coordination : bond 0.24020 ( 32) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.80035 ( 16) covalent geometry : bond 0.00226 (24872) covalent geometry : angle 0.50034 (33752) *********************** 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 296 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 2.601 Fit side-chains REVERT: A 39 LYS cc_start: 0.6796 (mttm) cc_final: 0.6394 (mttm) REVERT: A 53 GLN cc_start: 0.7635 (mt0) cc_final: 0.7095 (mm110) REVERT: A 115 GLU cc_start: 0.8369 (tp30) cc_final: 0.8041 (tp30) REVERT: A 172 GLU cc_start: 0.7431 (tt0) cc_final: 0.6990 (tm-30) REVERT: A 259 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7805 (ttmp) REVERT: B 53 GLN cc_start: 0.7743 (mt0) cc_final: 0.7204 (mm-40) REVERT: B 172 GLU cc_start: 0.7767 (tp30) cc_final: 0.6876 (OUTLIER) REVERT: B 312 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7334 (tp30) REVERT: B 315 ARG cc_start: 0.7409 (ttt90) cc_final: 0.6920 (mtp-110) REVERT: C 39 LYS cc_start: 0.6775 (mttm) cc_final: 0.6345 (mttm) REVERT: C 53 GLN cc_start: 0.7658 (mt0) cc_final: 0.7114 (mm110) REVERT: C 115 GLU cc_start: 0.8206 (tp30) cc_final: 0.7742 (tp30) REVERT: C 172 GLU cc_start: 0.7520 (tt0) cc_final: 0.7148 (tm-30) REVERT: D 39 LYS cc_start: 0.6857 (mttm) cc_final: 0.6627 (mmtp) REVERT: D 53 GLN cc_start: 0.7664 (mt0) cc_final: 0.7115 (mm110) REVERT: D 115 GLU cc_start: 0.8205 (tp30) cc_final: 0.7738 (tp30) REVERT: E 173 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.5882 (ttm170) REVERT: E 281 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7130 (ttm110) REVERT: E 283 MET cc_start: 0.8756 (mtp) cc_final: 0.8504 (mtp) REVERT: F 88 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: F 173 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.5847 (ttm170) REVERT: F 283 MET cc_start: 0.8754 (mtp) cc_final: 0.8487 (mtp) REVERT: G 173 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.5827 (ttm170) REVERT: H 88 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: H 173 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.5900 (ttm170) REVERT: H 338 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7010 (mtt180) outliers start: 63 outliers final: 45 residues processed: 287 average time/residue: 1.5051 time to fit residues: 490.6642 Evaluate side-chains 282 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 2.669 ------------------------------------------------------------------------------- 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 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 325 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 96 SER 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 96 SER Chi-restraints excluded: chain D residue 172 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 358 VAL Chi-restraints excluded: chain E residue 389 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 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 217 VAL 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 55 LEU Chi-restraints excluded: chain H residue 88 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 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 7.9990 chunk 276 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 115 optimal weight: 0.0010 chunk 35 optimal weight: 0.9980 chunk 272 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 HIS F 410 ASN G 271 HIS H 53 GLN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 HIS H 410 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124336 restraints weight = 24027.112| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.60 r_work: 0.3406 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.907 24912 Z= 0.365 Angle : 0.547 7.671 33768 Z= 0.283 Chirality : 0.046 0.221 3688 Planarity : 0.004 0.052 4496 Dihedral : 7.518 59.627 3758 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.52 % Allowed : 21.48 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3136 helix: 1.30 (0.15), residues: 1232 sheet: 0.13 (0.25), residues: 368 loop : -0.98 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.009 0.001 HIS E 251 PHE 0.014 0.002 PHE A 31 TYR 0.011 0.001 TYR F 333 ARG 0.002 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 1034) hydrogen bonds : angle 4.02992 ( 2853) metal coordination : bond 0.27645 ( 32) SS BOND : bond 0.00327 ( 8) SS BOND : angle 0.95319 ( 16) covalent geometry : bond 0.00365 (24872) covalent geometry : angle 0.54644 (33752) ********************** 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 291 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 2.603 Fit side-chains REVERT: A 39 LYS cc_start: 0.6871 (mttm) cc_final: 0.6438 (mttm) REVERT: A 53 GLN cc_start: 0.7678 (mt0) cc_final: 0.7153 (mm110) REVERT: A 66 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.4991 (ttm170) REVERT: A 115 GLU cc_start: 0.8397 (tp30) cc_final: 0.8123 (tp30) REVERT: A 172 GLU cc_start: 0.7435 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 259 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7846 (ttmp) REVERT: B 53 GLN cc_start: 0.7736 (mt0) cc_final: 0.7182 (mm110) REVERT: B 66 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5003 (ttm170) REVERT: B 131 GLU cc_start: 0.6885 (pp20) cc_final: 0.6395 (pp20) REVERT: B 172 GLU cc_start: 0.7738 (tp30) cc_final: 0.6848 (OUTLIER) REVERT: B 312 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7381 (tp30) REVERT: B 315 ARG cc_start: 0.7449 (ttt90) cc_final: 0.6955 (mtp-110) REVERT: C 53 GLN cc_start: 0.7709 (mt0) cc_final: 0.7168 (mm110) REVERT: C 115 GLU cc_start: 0.8259 (tp30) cc_final: 0.7819 (tp30) REVERT: C 172 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: D 39 LYS cc_start: 0.6916 (mttm) cc_final: 0.6695 (mmtp) REVERT: D 53 GLN cc_start: 0.7687 (mt0) cc_final: 0.7163 (tp40) REVERT: D 66 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5075 (ttm170) REVERT: D 115 GLU cc_start: 0.8238 (tp30) cc_final: 0.7813 (tp30) REVERT: D 131 GLU cc_start: 0.6882 (pp20) cc_final: 0.6387 (pp20) REVERT: E 173 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.5912 (ttm170) REVERT: E 281 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.7189 (ttm110) REVERT: E 283 MET cc_start: 0.8778 (mtp) cc_final: 0.8532 (mtp) REVERT: F 88 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: F 173 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.5840 (ttm170) REVERT: F 283 MET cc_start: 0.8777 (mtp) cc_final: 0.8536 (mtp) REVERT: F 303 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7368 (mmtt) REVERT: G 173 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.5881 (ttm170) REVERT: H 88 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: H 173 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.5888 (ttm170) REVERT: H 338 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7127 (mtt180) outliers start: 61 outliers final: 45 residues processed: 286 average time/residue: 1.5723 time to fit residues: 511.1832 Evaluate side-chains 286 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 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 251 HIS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL 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 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 94 SER 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 358 VAL Chi-restraints excluded: chain D residue 376 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 313 VAL Chi-restraints excluded: chain E residue 358 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 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 358 VAL Chi-restraints excluded: chain F residue 389 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 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 88 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 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 GLN F 271 HIS G 271 HIS H 53 GLN H 271 HIS 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 = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124345 restraints weight = 24677.609| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.82 r_work: 0.3408 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.756 24912 Z= 0.316 Angle : 0.547 7.739 33768 Z= 0.283 Chirality : 0.046 0.220 3688 Planarity : 0.004 0.050 4496 Dihedral : 7.470 59.859 3758 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.69 % Allowed : 21.11 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3136 helix: 1.27 (0.15), residues: 1232 sheet: 0.09 (0.25), residues: 368 loop : -0.98 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.011 0.001 HIS F 251 PHE 0.014 0.001 PHE A 31 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 1034) hydrogen bonds : angle 4.04430 ( 2853) metal coordination : bond 0.23140 ( 32) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.94754 ( 16) covalent geometry : bond 0.00359 (24872) covalent geometry : angle 0.54695 (33752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16867.33 seconds wall clock time: 291 minutes 8.62 seconds (17468.62 seconds total)