Starting phenix.real_space_refine on Sat Jun 21 05:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j85_36060/06_2025/8j85_36060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j85_36060/06_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_36060/06_2025/8j85_36060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j85_36060/06_2025/8j85_36060.map" model { file = "/net/cci-nas-00/data/ceres_data/8j85_36060/06_2025/8j85_36060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j85_36060/06_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-5710/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: 15.87, per 1000 atoms: 0.65 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: 6.23 Conformation dependent library (CDL) restraints added in 3.5 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: 2.80 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: 9.06 Time building geometry restraints manager: 7.39 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: 4.370 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: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 62.850 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.990 ------------------------------------------------------------------------------- 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 : 2.703 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: 2.1109 time to fit residues: 1157.3629 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 : 2.445 ------------------------------------------------------------------------------- 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 = 0.126476 restraints weight = 25366.907| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.66 r_work: 0.3440 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 1.39054 ( 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 : 2.695 Fit side-chains REVERT: A 315 ARG cc_start: 0.7329 (ttt90) cc_final: 0.6933 (mtp-110) REVERT: B 172 GLU cc_start: 0.7857 (tp30) cc_final: 0.6915 (tm-30) REVERT: B 312 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7084 (tp30) REVERT: B 315 ARG cc_start: 0.7309 (ttt90) cc_final: 0.6932 (mtp-110) REVERT: C 31 PHE cc_start: 0.8300 (t80) cc_final: 0.7894 (t80) REVERT: C 315 ARG cc_start: 0.7330 (ttt90) cc_final: 0.6912 (mtp-110) REVERT: D 172 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6975 (tm-30) REVERT: D 315 ARG cc_start: 0.7239 (ttt90) cc_final: 0.6862 (mtp-110) REVERT: E 93 GLN cc_start: 0.7446 (mp10) cc_final: 0.6953 (mm-40) REVERT: E 173 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6018 (ttm170) REVERT: E 283 MET cc_start: 0.8776 (mtp) cc_final: 0.8486 (mtp) REVERT: E 338 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7251 (mtt180) REVERT: E 385 ASP cc_start: 0.8147 (p0) cc_final: 0.7877 (p0) REVERT: F 93 GLN cc_start: 0.7433 (mp10) cc_final: 0.6950 (mm-40) REVERT: F 173 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6110 (ttm170) REVERT: F 283 MET cc_start: 0.8781 (mtp) cc_final: 0.8474 (mtp) REVERT: F 338 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7239 (mtt180) REVERT: F 385 ASP cc_start: 0.8123 (p0) cc_final: 0.7862 (p0) REVERT: G 93 GLN cc_start: 0.7395 (mp10) cc_final: 0.6868 (mm-40) REVERT: G 173 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: G 283 MET cc_start: 0.8791 (mtp) cc_final: 0.8499 (mtp) REVERT: G 338 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: G 385 ASP cc_start: 0.8080 (p0) cc_final: 0.7819 (p0) REVERT: H 88 GLU cc_start: 0.7525 (pt0) cc_final: 0.7316 (pt0) REVERT: H 93 GLN cc_start: 0.7411 (mp10) cc_final: 0.6902 (mm-40) REVERT: H 173 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6190 (ttm170) REVERT: H 338 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7269 (mtt180) REVERT: H 385 ASP cc_start: 0.8090 (p0) cc_final: 0.7852 (p0) outliers start: 50 outliers final: 18 residues processed: 299 average time/residue: 1.6665 time to fit residues: 566.2420 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 : 2.818 ------------------------------------------------------------------------------- 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: 8.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 68 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126629 restraints weight = 24577.007| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.86 r_work: 0.3429 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.046 24912 Z= 0.566 Angle : 0.507 7.666 33768 Z= 0.264 Chirality : 0.045 0.222 3688 Planarity : 0.004 0.049 4496 Dihedral : 8.470 89.764 3758 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.23 % Allowed : 20.90 % Favored : 75.87 % 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: 0.13 (0.14), residues: 3136 helix: 1.28 (0.15), residues: 1232 sheet: 0.70 (0.25), residues: 400 loop : -1.13 (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 0.009 0.001 PHE E 294 TYR 0.010 0.001 TYR A 333 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 1034) hydrogen bonds : angle 4.11422 ( 2853) metal coordination : bond 0.46207 ( 32) SS BOND : bond 0.00368 ( 8) SS BOND : angle 1.19923 ( 16) covalent geometry : bond 0.00283 (24872) covalent geometry : angle 0.50595 (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 313 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 235 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7681 (mt0) cc_final: 0.7182 (mm110) REVERT: A 131 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: A 172 GLU cc_start: 0.7552 (tt0) cc_final: 0.7050 (tm-30) REVERT: A 315 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6953 (mtp-110) REVERT: B 53 GLN cc_start: 0.7693 (mt0) cc_final: 0.7198 (mm110) REVERT: B 131 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6570 (pp20) REVERT: B 172 GLU cc_start: 0.7903 (tp30) cc_final: 0.7013 (tm-30) REVERT: B 312 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7187 (tp30) REVERT: B 315 ARG cc_start: 0.7349 (ttt90) cc_final: 0.6934 (mtp-110) REVERT: C 53 GLN cc_start: 0.7700 (mt0) cc_final: 0.7180 (mm110) REVERT: C 131 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6577 (pp20) REVERT: C 172 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: C 315 ARG cc_start: 0.7360 (ttt90) cc_final: 0.6973 (mtp-110) REVERT: D 53 GLN cc_start: 0.7671 (mt0) cc_final: 0.7173 (tp40) REVERT: D 131 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6546 (pp20) REVERT: D 172 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: D 315 ARG cc_start: 0.7374 (ttt90) cc_final: 0.6964 (mtp-110) REVERT: E 173 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6030 (ttm170) REVERT: E 283 MET cc_start: 0.8780 (mtp) cc_final: 0.8542 (mtp) REVERT: E 338 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7273 (mtt180) REVERT: E 385 ASP cc_start: 0.8271 (p0) cc_final: 0.7982 (p0) REVERT: F 173 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6106 (ttm170) REVERT: F 283 MET cc_start: 0.8777 (mtp) cc_final: 0.8532 (mtp) REVERT: F 338 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7257 (mtt180) REVERT: F 385 ASP cc_start: 0.8228 (p0) cc_final: 0.8017 (p0) REVERT: G 173 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6026 (ttm170) REVERT: G 338 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7280 (mtt180) REVERT: G 385 ASP cc_start: 0.8225 (p0) cc_final: 0.7998 (p0) REVERT: H 173 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6186 (ttm170) REVERT: H 338 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7280 (mtt180) REVERT: H 385 ASP cc_start: 0.8246 (p0) cc_final: 0.8020 (p0) outliers start: 78 outliers final: 36 residues processed: 297 average time/residue: 2.1468 time to fit residues: 722.4920 Evaluate side-chains 268 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 3.382 ------------------------------------------------------------------------------- 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 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 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 358 VAL Chi-restraints excluded: chain D residue 76 LEU 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 E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 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 172 GLU 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: 0.9990 chunk 274 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122438 restraints weight = 25109.933| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.75 r_work: 0.3379 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24912 Z= 0.230 Angle : 0.610 8.743 33768 Z= 0.323 Chirality : 0.050 0.218 3688 Planarity : 0.005 0.056 4496 Dihedral : 8.745 82.710 3758 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.72 % Allowed : 18.83 % Favored : 76.45 % 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: -0.13 (0.14), residues: 3136 helix: 0.99 (0.15), residues: 1232 sheet: 0.44 (0.25), residues: 400 loop : -1.16 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.030 0.002 HIS E 251 PHE 0.012 0.002 PHE A 122 TYR 0.014 0.002 TYR B 95 ARG 0.004 0.001 ARG G 109 Details of bonding type rmsd hydrogen bonds : bond 0.06060 ( 1034) hydrogen bonds : angle 4.38624 ( 2853) metal coordination : bond 0.03201 ( 32) SS BOND : bond 0.00395 ( 8) SS BOND : angle 1.31998 ( 16) covalent geometry : bond 0.00547 (24872) covalent geometry : angle 0.60987 (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 340 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 226 time to evaluate : 2.517 Fit side-chains REVERT: A 53 GLN cc_start: 0.7881 (mt0) cc_final: 0.7354 (tp40) REVERT: A 131 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6600 (pp20) REVERT: A 172 GLU cc_start: 0.7513 (tt0) cc_final: 0.7045 (tm-30) REVERT: A 259 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7788 (ttmp) REVERT: A 315 ARG cc_start: 0.7445 (ttt90) cc_final: 0.7017 (mtp-110) REVERT: B 53 GLN cc_start: 0.7883 (mt0) cc_final: 0.7335 (mm110) REVERT: B 131 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6591 (pp20) REVERT: B 172 GLU cc_start: 0.7867 (tp30) cc_final: 0.6957 (tm-30) REVERT: B 259 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7782 (ttmp) REVERT: B 312 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7283 (tp30) REVERT: B 315 ARG cc_start: 0.7443 (ttt90) cc_final: 0.6996 (mtp-110) REVERT: C 53 GLN cc_start: 0.7890 (mt0) cc_final: 0.7346 (tp40) REVERT: C 66 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5036 (ttm170) REVERT: C 131 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: C 172 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: C 259 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7791 (ttmp) REVERT: C 315 ARG cc_start: 0.7390 (ttt90) cc_final: 0.6981 (mtp-110) REVERT: C 385 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6875 (p0) REVERT: D 53 GLN cc_start: 0.7906 (mt0) cc_final: 0.7389 (tp40) REVERT: D 131 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6595 (pp20) REVERT: D 259 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7816 (ttmp) REVERT: D 315 ARG cc_start: 0.7427 (ttt90) cc_final: 0.7009 (mtp-110) REVERT: D 385 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6896 (p0) REVERT: E 31 PHE cc_start: 0.7700 (t80) cc_final: 0.7418 (t80) REVERT: E 283 MET cc_start: 0.8804 (mtp) cc_final: 0.8539 (mtp) REVERT: E 338 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: F 31 PHE cc_start: 0.7689 (t80) cc_final: 0.7428 (t80) REVERT: F 88 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: F 119 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8324 (mmt) REVERT: F 283 MET cc_start: 0.8814 (mtp) cc_final: 0.8531 (mtp) REVERT: F 338 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7209 (mtt180) REVERT: G 31 PHE cc_start: 0.7710 (t80) cc_final: 0.7374 (t80) REVERT: G 338 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7227 (mtt180) REVERT: H 173 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6022 (ttm170) REVERT: H 338 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7188 (mtt180) outliers start: 114 outliers final: 51 residues processed: 320 average time/residue: 1.5534 time to fit residues: 563.2198 Evaluate side-chains 286 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 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 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 88 GLU 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 119 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 217 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 26 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS G 271 HIS H 271 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121654 restraints weight = 25416.996| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.77 r_work: 0.3376 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.715 24912 Z= 0.383 Angle : 0.619 8.683 33768 Z= 0.327 Chirality : 0.050 0.219 3688 Planarity : 0.005 0.055 4496 Dihedral : 8.474 72.023 3758 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.88 % Allowed : 18.42 % Favored : 76.70 % 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: -0.35 (0.14), residues: 3136 helix: 0.80 (0.15), residues: 1232 sheet: 0.00 (0.24), residues: 408 loop : -1.17 (0.14), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 79 HIS 0.023 0.002 HIS G 251 PHE 0.014 0.002 PHE A 31 TYR 0.014 0.002 TYR A 95 ARG 0.002 0.001 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 1034) hydrogen bonds : angle 4.41478 ( 2853) metal coordination : bond 0.25154 ( 32) SS BOND : bond 0.00405 ( 8) SS BOND : angle 1.26952 ( 16) covalent geometry : bond 0.00571 (24872) covalent geometry : angle 0.61810 (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 330 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 212 time to evaluate : 2.653 Fit side-chains REVERT: A 53 GLN cc_start: 0.7885 (mt0) cc_final: 0.7376 (tp40) REVERT: A 131 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6741 (pp20) REVERT: A 172 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: A 259 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7800 (ttmp) REVERT: A 303 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7439 (tppt) REVERT: A 315 ARG cc_start: 0.7476 (ttt90) cc_final: 0.7031 (mtp-110) REVERT: A 385 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.7000 (p0) REVERT: B 53 GLN cc_start: 0.7877 (mt0) cc_final: 0.7339 (tp40) REVERT: B 172 GLU cc_start: 0.7767 (tp30) cc_final: 0.6886 (tm-30) REVERT: B 259 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7874 (ttmp) REVERT: B 303 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7467 (tppt) REVERT: B 312 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7325 (tp30) REVERT: B 315 ARG cc_start: 0.7447 (ttt90) cc_final: 0.7057 (mtp-110) REVERT: C 53 GLN cc_start: 0.7877 (mt0) cc_final: 0.7338 (tp40) REVERT: C 131 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: C 172 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: C 259 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7876 (ttmp) REVERT: C 303 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7504 (tppt) REVERT: C 385 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7016 (p0) REVERT: D 53 GLN cc_start: 0.7914 (mt0) cc_final: 0.7387 (tp40) REVERT: D 131 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: D 259 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7804 (ttmp) REVERT: D 303 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7414 (tppt) REVERT: D 385 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7014 (p0) REVERT: E 31 PHE cc_start: 0.7682 (t80) cc_final: 0.7369 (t80) REVERT: E 119 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8356 (mmt) REVERT: E 173 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.5805 (ttm170) REVERT: E 281 ARG cc_start: 0.7809 (ttp-110) cc_final: 0.7253 (ttm110) REVERT: E 283 MET cc_start: 0.8806 (mtp) cc_final: 0.8517 (mtp) REVERT: E 338 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7224 (mtt180) REVERT: F 88 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: F 173 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.5795 (ttm170) REVERT: F 283 MET cc_start: 0.8806 (mtp) cc_final: 0.8503 (mtp) REVERT: F 338 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: G 31 PHE cc_start: 0.7723 (t80) cc_final: 0.7430 (t80) REVERT: G 173 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.5818 (ttm170) REVERT: G 338 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7225 (mtt180) REVERT: H 88 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: H 119 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8362 (mmt) REVERT: H 338 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7255 (mtt180) outliers start: 118 outliers final: 58 residues processed: 301 average time/residue: 2.0166 time to fit residues: 689.3417 Evaluate side-chains 293 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 208 time to evaluate : 3.413 ------------------------------------------------------------------------------- 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 172 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 30 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 303 LYS 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 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 362 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 74 VAL 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 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 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 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: 6.9990 chunk 214 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 232 optimal weight: 0.0030 chunk 182 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 HIS H 271 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124829 restraints weight = 24041.517| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.59 r_work: 0.3408 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.905 24912 Z= 0.397 Angle : 0.519 7.610 33768 Z= 0.270 Chirality : 0.046 0.219 3688 Planarity : 0.004 0.049 4496 Dihedral : 7.677 59.273 3758 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.77 % Allowed : 19.78 % Favored : 76.45 % 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: -0.06 (0.14), residues: 3136 helix: 1.14 (0.15), residues: 1224 sheet: 0.05 (0.24), residues: 408 loop : -1.07 (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 0.010 0.001 PHE B 31 TYR 0.010 0.001 TYR F 333 ARG 0.002 0.000 ARG G 109 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 1034) hydrogen bonds : angle 4.10114 ( 2853) metal coordination : bond 0.31332 ( 32) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.97932 ( 16) covalent geometry : bond 0.00308 (24872) covalent geometry : angle 0.51830 (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 318 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 227 time to evaluate : 2.702 Fit side-chains REVERT: A 53 GLN cc_start: 0.7848 (mt0) cc_final: 0.7296 (tp40) REVERT: A 66 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.4539 (ttm170) REVERT: A 172 GLU cc_start: 0.7413 (tt0) cc_final: 0.6985 (tm-30) REVERT: A 259 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7780 (ttmp) REVERT: A 385 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6974 (p0) REVERT: B 34 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7992 (ttm170) REVERT: B 53 GLN cc_start: 0.7826 (mt0) cc_final: 0.7325 (mm-40) REVERT: B 66 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.4539 (ttm170) REVERT: B 172 GLU cc_start: 0.7735 (tp30) cc_final: 0.6845 (tm-30) REVERT: B 312 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7296 (tp30) REVERT: B 315 ARG cc_start: 0.7418 (ttt90) cc_final: 0.6988 (mtp-110) REVERT: C 34 ARG cc_start: 0.8287 (ttm170) cc_final: 0.8060 (ttm170) REVERT: C 53 GLN cc_start: 0.7848 (mt0) cc_final: 0.7300 (tp40) REVERT: C 172 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: D 34 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8061 (ttm170) REVERT: D 53 GLN cc_start: 0.7834 (mt0) cc_final: 0.7287 (tp40) REVERT: D 419 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8801 (ttt) REVERT: E 173 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.5825 (ttm170) REVERT: E 281 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7199 (ttm110) REVERT: E 338 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7211 (mtt180) REVERT: F 88 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: F 173 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5784 (ttm170) REVERT: F 283 MET cc_start: 0.8780 (mtp) cc_final: 0.8511 (mtp) REVERT: F 338 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7198 (mtt180) REVERT: G 31 PHE cc_start: 0.7648 (t80) cc_final: 0.7344 (t80) REVERT: G 173 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.5812 (ttm170) REVERT: G 338 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7190 (mtt180) REVERT: H 88 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: H 173 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6024 (ttm170) REVERT: H 338 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7215 (mtt180) outliers start: 91 outliers final: 49 residues processed: 304 average time/residue: 1.6032 time to fit residues: 551.4097 Evaluate side-chains 280 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 30 LEU 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 358 VAL Chi-restraints excluded: chain B residue 376 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 C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU 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 D residue 419 MET 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 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 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 55 LEU Chi-restraints excluded: chain H residue 76 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS E 335 ASN F 271 HIS F 335 ASN G 53 GLN G 271 HIS G 335 ASN H 271 HIS H 335 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124040 restraints weight = 24888.267| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.80 r_work: 0.3400 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.749 24912 Z= 0.351 Angle : 0.541 7.841 33768 Z= 0.283 Chirality : 0.047 0.219 3688 Planarity : 0.005 0.051 4496 Dihedral : 7.583 59.434 3758 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.14 % Allowed : 19.58 % Favored : 76.28 % 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: -0.13 (0.14), residues: 3136 helix: 1.10 (0.15), residues: 1232 sheet: 0.09 (0.26), residues: 360 loop : -1.12 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 79 HIS 0.014 0.001 HIS G 251 PHE 0.012 0.001 PHE D 31 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 ARG D 149 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 1034) hydrogen bonds : angle 4.12901 ( 2853) metal coordination : bond 0.26273 ( 32) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.00454 ( 16) covalent geometry : bond 0.00371 (24872) covalent geometry : angle 0.54065 (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 322 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 222 time to evaluate : 2.535 Fit side-chains REVERT: A 53 GLN cc_start: 0.7868 (mt0) cc_final: 0.7336 (tp40) REVERT: A 172 GLU cc_start: 0.7443 (tt0) cc_final: 0.7015 (tm-30) REVERT: A 259 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (ttmp) REVERT: B 53 GLN cc_start: 0.7865 (mt0) cc_final: 0.7343 (tp40) REVERT: B 131 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: B 172 GLU cc_start: 0.7766 (tp30) cc_final: 0.6883 (tm-30) REVERT: B 259 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7815 (ttmp) REVERT: B 312 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7398 (tp30) REVERT: B 315 ARG cc_start: 0.7421 (ttt90) cc_final: 0.6983 (mtp-110) REVERT: C 34 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8050 (ttm170) REVERT: C 39 LYS cc_start: 0.6769 (mttm) cc_final: 0.6330 (mttm) REVERT: C 53 GLN cc_start: 0.7852 (mt0) cc_final: 0.7321 (tp40) REVERT: C 172 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: C 259 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7811 (ttmp) REVERT: D 53 GLN cc_start: 0.7851 (mt0) cc_final: 0.7313 (tp40) REVERT: D 259 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7819 (ttmp) REVERT: E 173 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.5835 (ttm170) REVERT: E 281 ARG cc_start: 0.7792 (ttp-110) cc_final: 0.7225 (ttm110) REVERT: E 283 MET cc_start: 0.8769 (mtp) cc_final: 0.8534 (mtp) REVERT: E 338 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7172 (mtt180) REVERT: F 88 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: F 173 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.5835 (ttm170) REVERT: F 283 MET cc_start: 0.8789 (mtp) cc_final: 0.8547 (mtp) REVERT: F 303 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7355 (mmtt) REVERT: F 338 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7167 (mtt180) REVERT: G 31 PHE cc_start: 0.7664 (t80) cc_final: 0.7356 (t80) REVERT: G 173 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5825 (ttm170) REVERT: G 303 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7329 (mmtt) REVERT: G 338 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7142 (mtt180) REVERT: H 88 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: H 173 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.5916 (ttm170) REVERT: H 303 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7351 (mmtt) REVERT: H 338 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7163 (mtt180) outliers start: 100 outliers final: 51 residues processed: 301 average time/residue: 1.6717 time to fit residues: 569.6001 Evaluate side-chains 289 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 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 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU 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 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 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 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 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 258 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS G 271 HIS H 271 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123921 restraints weight = 23359.832| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.55 r_work: 0.3399 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.909 24912 Z= 0.409 Angle : 0.552 7.777 33768 Z= 0.288 Chirality : 0.047 0.221 3688 Planarity : 0.005 0.052 4496 Dihedral : 7.616 59.768 3758 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.85 % Allowed : 19.78 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.14), residues: 3136 helix: 1.08 (0.15), residues: 1232 sheet: 0.06 (0.25), residues: 360 loop : -1.10 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 79 HIS 0.005 0.001 HIS B 251 PHE 0.013 0.002 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 0.04992 ( 1034) hydrogen bonds : angle 4.13272 ( 2853) metal coordination : bond 0.31341 ( 32) SS BOND : bond 0.00329 ( 8) SS BOND : angle 1.00248 ( 16) covalent geometry : bond 0.00390 (24872) covalent geometry : angle 0.55158 (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 320 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 227 time to evaluate : 2.684 Fit side-chains REVERT: A 53 GLN cc_start: 0.7872 (mt0) cc_final: 0.7332 (tp40) REVERT: A 115 GLU cc_start: 0.8383 (tp30) cc_final: 0.8153 (tp30) REVERT: A 172 GLU cc_start: 0.7390 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 259 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7795 (ttmp) REVERT: B 53 GLN cc_start: 0.7867 (mt0) cc_final: 0.7334 (tp40) REVERT: B 66 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.4824 (ttm170) REVERT: B 115 GLU cc_start: 0.8359 (tp30) cc_final: 0.8153 (tp30) REVERT: B 131 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6787 (pp20) REVERT: B 172 GLU cc_start: 0.7729 (tp30) cc_final: 0.6854 (tm-30) REVERT: B 259 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7811 (ttmp) REVERT: B 312 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7400 (tp30) REVERT: B 315 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6956 (mtp-110) REVERT: C 34 ARG cc_start: 0.8274 (ttm170) cc_final: 0.8051 (ttm170) REVERT: C 53 GLN cc_start: 0.7873 (mt0) cc_final: 0.7332 (tp40) REVERT: C 115 GLU cc_start: 0.8367 (tp30) cc_final: 0.8150 (tp30) REVERT: C 172 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: C 259 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7814 (ttmp) REVERT: D 53 GLN cc_start: 0.7850 (mt0) cc_final: 0.7308 (tp40) REVERT: D 115 GLU cc_start: 0.8365 (tp30) cc_final: 0.8153 (tp30) REVERT: D 259 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7815 (ttmp) REVERT: E 173 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.5835 (ttm170) REVERT: E 281 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7218 (ttm110) REVERT: E 283 MET cc_start: 0.8775 (mtp) cc_final: 0.8534 (mtp) REVERT: E 303 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7365 (mmtt) REVERT: E 338 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7211 (mtt180) REVERT: F 88 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: F 173 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.5819 (ttm170) REVERT: F 283 MET cc_start: 0.8784 (mtp) cc_final: 0.8529 (mtp) REVERT: F 303 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7395 (mmtt) REVERT: F 338 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7161 (mtt180) REVERT: G 88 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: G 173 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5858 (ttm170) REVERT: G 303 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: G 338 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7155 (mtt180) REVERT: H 88 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7413 (pt0) REVERT: H 173 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.5909 (ttm170) REVERT: H 303 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7377 (mmtt) REVERT: H 338 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7140 (mtt180) outliers start: 93 outliers final: 56 residues processed: 306 average time/residue: 1.6906 time to fit residues: 586.1349 Evaluate side-chains 299 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 30 LEU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 325 ILE 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 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 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 303 LYS 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 23 VAL Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 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: 3.9990 chunk 175 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS G 53 GLN G 271 HIS H 53 GLN H 271 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.147241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122761 restraints weight = 24690.583| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.78 r_work: 0.3378 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.727 24912 Z= 0.364 Angle : 0.591 8.101 33768 Z= 0.309 Chirality : 0.049 0.220 3688 Planarity : 0.005 0.053 4496 Dihedral : 7.935 59.892 3758 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.10 % Allowed : 19.58 % Favored : 76.32 % 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: -0.27 (0.14), residues: 3136 helix: 0.97 (0.15), residues: 1232 sheet: -0.08 (0.25), residues: 360 loop : -1.16 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.014 0.002 HIS G 251 PHE 0.013 0.002 PHE D 31 TYR 0.012 0.002 TYR H 333 ARG 0.002 0.000 ARG G 100 Details of bonding type rmsd hydrogen bonds : bond 0.05554 ( 1034) hydrogen bonds : angle 4.24600 ( 2853) metal coordination : bond 0.25394 ( 32) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.10254 ( 16) covalent geometry : bond 0.00481 (24872) covalent geometry : angle 0.59100 (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 320 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 221 time to evaluate : 2.734 Fit side-chains REVERT: A 53 GLN cc_start: 0.7871 (mt0) cc_final: 0.7339 (tp40) REVERT: A 66 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5096 (ttm170) REVERT: A 115 GLU cc_start: 0.8396 (tp30) cc_final: 0.8168 (tp30) REVERT: A 172 GLU cc_start: 0.7406 (tt0) cc_final: 0.6992 (tm-30) REVERT: A 259 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7805 (ttmp) REVERT: B 53 GLN cc_start: 0.7875 (mt0) cc_final: 0.7354 (tp40) REVERT: B 66 ARG cc_start: 0.6099 (OUTLIER) cc_final: 0.4917 (ttm170) REVERT: B 115 GLU cc_start: 0.8375 (tp30) cc_final: 0.8172 (tp30) REVERT: B 131 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: B 172 GLU cc_start: 0.7732 (tp30) cc_final: 0.6917 (tm-30) REVERT: B 259 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7849 (ttmp) REVERT: B 312 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7423 (tp30) REVERT: B 315 ARG cc_start: 0.7441 (ttt90) cc_final: 0.7002 (mtp-110) REVERT: C 34 ARG cc_start: 0.8284 (ttm170) cc_final: 0.8073 (ttm170) REVERT: C 53 GLN cc_start: 0.7886 (mt0) cc_final: 0.7366 (tp40) REVERT: C 115 GLU cc_start: 0.8376 (tp30) cc_final: 0.8160 (tp30) REVERT: C 172 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: C 259 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7854 (ttmp) REVERT: D 53 GLN cc_start: 0.7860 (mt0) cc_final: 0.7313 (tp40) REVERT: D 115 GLU cc_start: 0.8371 (tp30) cc_final: 0.8163 (tp30) REVERT: D 259 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7857 (ttmp) REVERT: E 31 PHE cc_start: 0.7705 (t80) cc_final: 0.7425 (t80) REVERT: E 88 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: E 173 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5862 (ttm170) REVERT: E 281 ARG cc_start: 0.7812 (ttp-110) cc_final: 0.7248 (ttm110) REVERT: E 303 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7390 (mmtt) REVERT: E 338 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7186 (mtt180) REVERT: F 88 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: F 173 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.5873 (ttm170) REVERT: F 303 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: F 338 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: G 31 PHE cc_start: 0.7734 (t80) cc_final: 0.7444 (t80) REVERT: G 173 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5882 (ttm170) REVERT: G 303 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7389 (mmtt) REVERT: G 338 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7144 (mtt180) REVERT: H 88 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: H 173 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.5975 (ttm170) REVERT: H 303 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7406 (mmtt) REVERT: H 338 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7140 (mtt180) outliers start: 99 outliers final: 58 residues processed: 303 average time/residue: 1.6017 time to fit residues: 549.5586 Evaluate side-chains 297 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 216 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 30 LEU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 325 ILE 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 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 74 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 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 303 LYS 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 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 76 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 258 MET Chi-restraints excluded: chain H residue 283 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 0.0980 chunk 195 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 404 ASN E 53 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS F 271 HIS G 271 HIS H 271 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124138 restraints weight = 23814.094| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.57 r_work: 0.3404 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3222 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= 0.402 Angle : 0.550 7.708 33768 Z= 0.286 Chirality : 0.047 0.220 3688 Planarity : 0.005 0.050 4496 Dihedral : 7.598 59.197 3758 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.44 % Allowed : 20.20 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.14), residues: 3136 helix: 1.10 (0.15), residues: 1232 sheet: -0.04 (0.25), residues: 360 loop : -1.08 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.006 0.001 HIS D 251 PHE 0.013 0.001 PHE A 31 TYR 0.011 0.001 TYR A 95 ARG 0.002 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 1034) hydrogen bonds : angle 4.10041 ( 2853) metal coordination : bond 0.31080 ( 32) SS BOND : bond 0.00323 ( 8) SS BOND : angle 1.00369 ( 16) covalent geometry : bond 0.00362 (24872) covalent geometry : angle 0.54927 (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 311 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 2.389 Fit side-chains REVERT: A 53 GLN cc_start: 0.7878 (mt0) cc_final: 0.7337 (tp40) REVERT: A 66 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5145 (ttm170) REVERT: A 115 GLU cc_start: 0.8360 (tp30) cc_final: 0.8111 (tp30) REVERT: A 172 GLU cc_start: 0.7383 (tt0) cc_final: 0.6976 (tm-30) REVERT: A 259 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7783 (ttmp) REVERT: B 53 GLN cc_start: 0.7873 (mt0) cc_final: 0.7345 (tp40) REVERT: B 66 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.4898 (ttm170) REVERT: B 115 GLU cc_start: 0.8336 (tp30) cc_final: 0.8110 (tp30) REVERT: B 172 GLU cc_start: 0.7710 (tp30) cc_final: 0.6918 (tm-30) REVERT: B 259 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7806 (ttmp) REVERT: B 312 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7439 (tp30) REVERT: C 53 GLN cc_start: 0.7883 (mt0) cc_final: 0.7345 (tp40) REVERT: C 115 GLU cc_start: 0.8344 (tp30) cc_final: 0.8107 (tp30) REVERT: C 172 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: C 259 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7819 (ttmp) REVERT: D 53 GLN cc_start: 0.7842 (mt0) cc_final: 0.7294 (tp40) REVERT: D 115 GLU cc_start: 0.8343 (tp30) cc_final: 0.8107 (tp30) REVERT: D 259 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7815 (ttmp) REVERT: E 31 PHE cc_start: 0.7680 (t80) cc_final: 0.7354 (t80) REVERT: E 88 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: E 173 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5862 (ttm170) REVERT: E 281 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7231 (ttm110) REVERT: E 283 MET cc_start: 0.8789 (mtp) cc_final: 0.8549 (mtp) REVERT: E 303 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7370 (mmtt) REVERT: E 338 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7195 (mtt180) REVERT: F 88 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: F 173 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.5830 (ttm170) REVERT: F 283 MET cc_start: 0.8796 (mtp) cc_final: 0.8534 (mtp) REVERT: F 303 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7400 (mmtt) REVERT: F 338 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7178 (mtt180) REVERT: G 173 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5837 (ttm170) REVERT: G 303 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7356 (mmtt) REVERT: G 338 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7169 (mtt180) REVERT: H 88 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: H 173 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: H 303 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7381 (mmtt) REVERT: H 338 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7157 (mtt180) outliers start: 83 outliers final: 56 residues processed: 300 average time/residue: 1.7753 time to fit residues: 609.0752 Evaluate side-chains 297 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 219 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 30 LEU Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS 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 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 303 LYS 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 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 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 258 MET Chi-restraints excluded: chain H residue 283 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 164 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 232 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN E 251 HIS E 271 HIS F 271 HIS F 335 ASN G 271 HIS H 271 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124082 restraints weight = 24539.626| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.79 r_work: 0.3398 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.754 24912 Z= 0.349 Angle : 0.554 7.725 33768 Z= 0.288 Chirality : 0.047 0.219 3688 Planarity : 0.005 0.052 4496 Dihedral : 7.570 59.041 3758 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.39 % Allowed : 20.32 % Favored : 76.28 % 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: -0.12 (0.14), residues: 3136 helix: 1.13 (0.15), residues: 1232 sheet: -0.05 (0.26), residues: 360 loop : -1.09 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 79 HIS 0.013 0.001 HIS G 251 PHE 0.013 0.001 PHE A 31 TYR 0.011 0.001 TYR F 333 ARG 0.002 0.000 ARG A 149 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1034) hydrogen bonds : angle 4.08647 ( 2853) metal coordination : bond 0.26166 ( 32) SS BOND : bond 0.00325 ( 8) SS BOND : angle 1.00123 ( 16) covalent geometry : bond 0.00366 (24872) covalent geometry : angle 0.55404 (33752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20325.27 seconds wall clock time: 358 minutes 3.10 seconds (21483.10 seconds total)