Starting phenix.real_space_refine on Sun Jul 5 00:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihs_35454/07_2026/8ihs_35454.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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 15272 2.51 5 N 4432 2.21 5 O 4552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24352 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 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: 4.98, per 1000 atoms: 0.20 Number of scatterers: 24352 At special positions: 0 Unit cell: (147.05, 147.05, 102, 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 4552 8.00 N 4432 7.00 C 15272 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=2.04 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.04 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.04 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.04 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 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 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " 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 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " 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: 120 helices and 32 sheets defined 41.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.983A 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: 3.601A 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 102 through 120 removed outlier: 3.545A pdb=" N HIS B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.584A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.982A 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: 3.601A 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 102 through 120 removed outlier: 3.545A pdb=" N HIS C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.723A pdb=" N GLY C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.983A 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: 3.601A 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 102 through 120 removed outlier: 3.545A pdb=" N HIS D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 4.345A 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 204 Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY D 297 " --> pdb=" O THR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.982A 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: 3.601A 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 102 through 120 removed outlier: 3.545A pdb=" N HIS E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.724A pdb=" N GLY E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.626A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.547A pdb=" N THR E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 363 removed outlier: 3.983A 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 Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'F' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.726A 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 303 removed outlier: 3.724A pdb=" N GLY F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.982A 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 Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'G' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 4.345A 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 204 Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.725A 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 303 removed outlier: 3.723A pdb=" N GLY G 297 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR G 328 " --> pdb=" O LEU G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 363 removed outlier: 3.983A 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 Processing helix chain 'G' and resid 408 through 413 Processing helix chain 'H' and resid 102 through 120 removed outlier: 3.545A pdb=" N HIS H 106 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 4.346A 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 204 Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.583A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.724A 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 303 removed outlier: 3.724A pdb=" N GLY H 297 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 322 removed outlier: 3.627A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 336 removed outlier: 3.546A pdb=" N THR H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 363 removed outlier: 3.982A 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 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: 6.344A pdb=" N THR A 43 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 54 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.781A 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: 13.872A pdb=" N VAL A 23 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY A 71 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL A 25 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS A 73 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS A 27 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS A 75 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG A 29 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE A 31 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP A 79 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG A 126 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.987A pdb=" N VAL A 248 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU A 270 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA A 250 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 269 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR B 43 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 54 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.833A 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: 13.872A pdb=" N VAL B 23 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY B 71 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL B 25 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS B 73 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS B 27 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS B 75 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG B 29 " --> pdb=" O CYS B 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE B 31 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP B 79 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG B 126 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.653A pdb=" N ILE B 209 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N HIS B 251 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 211 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 248 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU B 270 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 250 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 269 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR C 43 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL C 54 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.835A 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: 13.873A pdb=" N VAL C 23 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY C 71 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL C 25 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS C 73 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 27 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS C 75 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG C 29 " --> pdb=" O CYS C 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE C 31 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP C 79 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG C 126 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.675A pdb=" N ILE C 209 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 251 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE C 211 " --> pdb=" O HIS C 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 248 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU C 270 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 250 " --> pdb=" O GLU C 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 269 " --> pdb=" O VAL C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR D 43 " --> pdb=" O VAL D 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL D 54 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.833A 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: 13.873A pdb=" N VAL D 23 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY D 71 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL D 25 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS D 73 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS D 27 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS D 75 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG D 29 " --> pdb=" O CYS D 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE D 31 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP D 79 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG D 126 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.100A 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: 6.675A pdb=" N ILE D 209 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS D 251 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE D 211 " --> pdb=" O HIS D 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL D 248 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU D 270 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 250 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 269 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR E 43 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 54 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 6.834A 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: 13.872A pdb=" N VAL E 23 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY E 71 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL E 25 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS E 73 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS E 27 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS E 75 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG E 29 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE E 31 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP E 79 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG E 126 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.100A 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: 6.675A pdb=" N ILE E 209 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS E 251 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 211 " --> pdb=" O HIS E 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL E 248 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU E 270 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA E 250 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 269 " --> pdb=" O VAL E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.621A pdb=" N THR F 43 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL F 54 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.833A 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: 13.873A pdb=" N VAL F 23 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY F 71 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 12.718A pdb=" N VAL F 25 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS F 73 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS F 27 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS F 75 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG F 29 " --> pdb=" O CYS F 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE F 31 " --> pdb=" O PRO F 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP F 79 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ARG F 126 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.675A pdb=" N ILE F 209 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS F 251 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 211 " --> pdb=" O HIS F 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL F 248 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU F 270 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 250 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE F 269 " --> pdb=" O VAL F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 removed outlier: 6.622A pdb=" N THR G 43 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL G 54 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.835A 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: 13.872A pdb=" N VAL G 23 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY G 71 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 12.720A pdb=" N VAL G 25 " --> pdb=" O GLY G 71 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N LYS G 73 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS G 27 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS G 75 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 29 " --> pdb=" O CYS G 75 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N PHE G 31 " --> pdb=" O PRO G 77 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP G 79 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG G 126 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.675A pdb=" N ILE G 209 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS G 251 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE G 211 " --> pdb=" O HIS G 251 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL G 248 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLU G 270 " --> pdb=" O VAL G 248 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA G 250 " --> pdb=" O GLU G 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE G 269 " --> pdb=" O VAL G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 6.623A pdb=" N THR H 43 " --> pdb=" O VAL H 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL H 54 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.833A 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: 13.873A pdb=" N VAL H 23 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 13.758A pdb=" N GLY H 71 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 12.719A pdb=" N VAL H 25 " --> pdb=" O GLY H 71 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LYS H 73 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS H 27 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N CYS H 75 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG H 29 " --> pdb=" O CYS H 75 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE H 31 " --> pdb=" O PRO H 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.349A 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: 6.329A pdb=" N TRP H 79 " --> pdb=" O SER H 124 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG H 126 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 7.100A 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: 6.675A pdb=" N ILE H 209 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS H 251 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE H 211 " --> pdb=" O HIS H 251 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL H 248 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 270 " --> pdb=" O VAL H 248 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA H 250 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 269 " --> pdb=" O VAL H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 999 hydrogen bonds defined for protein. 2685 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: 4.45 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8421 1.34 - 1.46: 5485 1.46 - 1.58: 10806 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 24848 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.385 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 24843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 33328 2.63 - 5.25: 343 5.25 - 7.88: 41 7.88 - 10.51: 0 10.51 - 13.13: 8 Bond angle restraints: 33720 Sorted by residual: angle pdb=" CAH 97U D 503 " pdb=" OAI 97U D 503 " pdb=" CAJ 97U D 503 " ideal model delta sigma weight residual 120.79 107.66 13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAH 97U C 503 " pdb=" OAI 97U C 503 " pdb=" CAJ 97U C 503 " ideal model delta sigma weight residual 120.79 107.68 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAH 97U A 503 " pdb=" OAI 97U A 503 " pdb=" CAJ 97U A 503 " ideal model delta sigma weight residual 120.79 107.71 13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CAH 97U B 503 " pdb=" OAI 97U B 503 " pdb=" CAJ 97U B 503 " ideal model delta sigma weight residual 120.79 107.81 12.98 3.00e+00 1.11e-01 1.87e+01 angle pdb=" N THR H 301 " pdb=" CA THR H 301 " pdb=" C THR H 301 " ideal model delta sigma weight residual 113.55 108.10 5.45 1.26e+00 6.30e-01 1.87e+01 ... (remaining 33715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 12584 16.25 - 32.50: 1430 32.50 - 48.76: 503 48.76 - 65.01: 130 65.01 - 81.26: 57 Dihedral angle restraints: 14704 sinusoidal: 5744 harmonic: 8960 Sorted by residual: dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.14 77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 75 " pdb=" CB CYS E 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 27 " pdb=" SG CYS A 27 " pdb=" SG CYS A 75 " pdb=" CB CYS A 75 " ideal model delta sinusoidal sigma weight residual 93.00 15.17 77.83 1 1.00e+01 1.00e-02 7.58e+01 ... (remaining 14701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3291 0.073 - 0.146: 377 0.146 - 0.219: 12 0.219 - 0.292: 0 0.292 - 0.364: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U H 503 " pdb=" N 97U H 503 " pdb=" C 97U H 503 " pdb=" CB 97U H 503 " both_signs ideal model delta sigma weight residual False 2.30 2.67 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA 97U G 503 " pdb=" N 97U G 503 " pdb=" C 97U G 503 " pdb=" CB 97U G 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA 97U E 503 " pdb=" N 97U E 503 " pdb=" C 97U E 503 " pdb=" CB 97U E 503 " both_signs ideal model delta sigma weight residual False 2.30 2.66 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3685 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 298 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ARG G 298 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG G 298 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE G 299 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 102 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO G 103 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 291 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 292 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 292 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 292 " -0.023 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 23 2.15 - 2.84: 7699 2.84 - 3.52: 30872 3.52 - 4.21: 58985 4.21 - 4.90: 105021 Nonbonded interactions: 202600 Sorted by model distance: nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.460 2.230 nonbonded pdb=" OQ1 KCX H 210 " pdb="ZN ZN H 502 " model vdw 1.528 2.230 nonbonded pdb="ZN ZN G 502 " pdb=" OAX 97U G 503 " model vdw 1.769 2.230 nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.789 2.230 nonbonded pdb="ZN ZN A 502 " pdb=" OAX 97U A 503 " model vdw 1.825 2.230 ... (remaining 202595 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: 0.09 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.820 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 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 : 0.009 0.472 24888 Z= 0.356 Angle : 0.649 13.133 33736 Z= 0.339 Chirality : 0.047 0.364 3688 Planarity : 0.005 0.041 4488 Dihedral : 16.619 81.261 9000 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.37 % Allowed : 19.66 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.15), residues: 3136 helix: 0.67 (0.15), residues: 1256 sheet: -0.58 (0.25), residues: 448 loop : -0.66 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 315 TYR 0.011 0.001 TYR C 333 PHE 0.013 0.002 PHE H 294 TRP 0.004 0.001 TRP H 79 HIS 0.011 0.001 HIS G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.28 (24848) covalent geometry : angle 0.64733 / 0.34 (33720) SS BOND : bond 0.00852 / 0.50 ( 8) SS BOND : angle 2.37509 / 1.33 ( 16) hydrogen bonds : bond 0.16419 / 11.30 ( 983) hydrogen bonds : angle 5.09486 / 3.63 ( 2685) metal coordination : bond 0.18535 / 11.92 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 457 time to evaluate : 0.856 Fit side-chains REVERT: E 44 LEU cc_start: 0.8128 (mp) cc_final: 0.7892 (mm) REVERT: E 172 GLU cc_start: 0.7459 (pt0) cc_final: 0.7085 (tt0) REVERT: E 174 LEU cc_start: 0.7722 (mt) cc_final: 0.7512 (mt) REVERT: E 281 ARG cc_start: 0.7358 (mtp180) cc_final: 0.7134 (mtm110) REVERT: E 327 GLN cc_start: 0.6857 (mp-120) cc_final: 0.6452 (mm-40) REVERT: F 44 LEU cc_start: 0.8116 (mp) cc_final: 0.7894 (mm) REVERT: F 155 LYS cc_start: 0.8035 (tptp) cc_final: 0.7828 (tptp) REVERT: F 172 GLU cc_start: 0.7454 (pt0) cc_final: 0.6935 (mm-30) REVERT: F 174 LEU cc_start: 0.7628 (mt) cc_final: 0.7409 (mt) REVERT: F 281 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7145 (mtm110) REVERT: F 327 GLN cc_start: 0.6872 (mp-120) cc_final: 0.6474 (mm-40) REVERT: G 44 LEU cc_start: 0.8140 (mp) cc_final: 0.7901 (mm) REVERT: G 155 LYS cc_start: 0.8043 (tptp) cc_final: 0.7839 (tptp) REVERT: G 172 GLU cc_start: 0.7450 (pt0) cc_final: 0.7064 (tt0) REVERT: G 174 LEU cc_start: 0.7697 (mt) cc_final: 0.7480 (mt) REVERT: G 207 ASP cc_start: 0.8385 (m-30) cc_final: 0.8139 (m-30) REVERT: G 281 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7191 (mtm110) REVERT: G 327 GLN cc_start: 0.6796 (mp-120) cc_final: 0.6399 (mm-40) REVERT: H 44 LEU cc_start: 0.8119 (mp) cc_final: 0.7873 (mm) REVERT: H 155 LYS cc_start: 0.8014 (tptp) cc_final: 0.7807 (tptp) REVERT: H 174 LEU cc_start: 0.7663 (mt) cc_final: 0.7459 (mt) REVERT: H 281 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7146 (mtm110) REVERT: H 327 GLN cc_start: 0.6826 (mp-120) cc_final: 0.6437 (mm-40) outliers start: 9 outliers final: 9 residues processed: 465 average time/residue: 0.6733 time to fit residues: 355.2866 Evaluate side-chains 374 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 365 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain H residue 251 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN D 404 ASN E 26 GLN E 53 GLN E 93 GLN E 404 ASN F 26 GLN F 53 GLN F 93 GLN F 404 ASN G 26 GLN G 53 GLN G 93 GLN G 404 ASN H 26 GLN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105748 restraints weight = 24053.618| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.60 r_work: 0.3142 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24888 Z= 0.179 Angle : 0.570 7.908 33736 Z= 0.306 Chirality : 0.047 0.233 3688 Planarity : 0.005 0.045 4488 Dihedral : 6.979 64.460 3675 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.31 % Allowed : 16.56 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3136 helix: 0.84 (0.15), residues: 1264 sheet: 0.04 (0.25), residues: 472 loop : -0.80 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 315 TYR 0.014 0.002 TYR H 244 PHE 0.016 0.002 PHE F 294 TRP 0.008 0.001 TRP H 289 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (24848) covalent geometry : angle 0.56992 / 0.31 (33720) SS BOND : bond 0.01043 / 0.61 ( 8) SS BOND : angle 0.87317 / 0.46 ( 16) hydrogen bonds : bond 0.05943 / 4.03 ( 983) hydrogen bonds : angle 3.86308 / 2.76 ( 2685) metal coordination : bond 0.00599 / 0.42 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 350 time to evaluate : 1.027 Fit side-chains REVERT: A 52 ARG cc_start: 0.7319 (mtm180) cc_final: 0.6836 (mpt-90) REVERT: A 270 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: B 270 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: C 270 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: D 270 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8278 (mm-30) REVERT: E 44 LEU cc_start: 0.8464 (mp) cc_final: 0.8152 (mm) REVERT: E 172 GLU cc_start: 0.7824 (pt0) cc_final: 0.7598 (pt0) REVERT: E 281 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7355 (mtm110) REVERT: E 414 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7760 (t70) REVERT: F 44 LEU cc_start: 0.8474 (mp) cc_final: 0.8177 (mm) REVERT: F 131 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: F 172 GLU cc_start: 0.7836 (pt0) cc_final: 0.7615 (pt0) REVERT: F 281 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7367 (mtm110) REVERT: F 414 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7780 (t70) REVERT: G 44 LEU cc_start: 0.8472 (mp) cc_final: 0.8175 (mm) REVERT: G 172 GLU cc_start: 0.7812 (pt0) cc_final: 0.7603 (pt0) REVERT: G 281 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7396 (mtm110) REVERT: G 414 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7751 (t70) REVERT: H 44 LEU cc_start: 0.8469 (mp) cc_final: 0.8158 (mm) REVERT: H 281 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7370 (mtm110) REVERT: H 414 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7780 (t70) outliers start: 80 outliers final: 37 residues processed: 400 average time/residue: 0.6682 time to fit residues: 304.8245 Evaluate side-chains 368 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 177 LEU 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 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 177 LEU 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 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 177 LEU 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 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 53 GLN G 93 GLN H 26 GLN H 53 GLN H 93 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104692 restraints weight = 24219.192| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.62 r_work: 0.3115 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24888 Z= 0.226 Angle : 0.614 9.897 33736 Z= 0.330 Chirality : 0.049 0.227 3688 Planarity : 0.006 0.047 4488 Dihedral : 7.346 59.501 3675 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.14 % Allowed : 15.52 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3136 helix: 0.73 (0.14), residues: 1264 sheet: 0.12 (0.27), residues: 432 loop : -0.96 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 247 TYR 0.016 0.002 TYR A 333 PHE 0.018 0.002 PHE H 294 TRP 0.009 0.002 TRP G 289 HIS 0.008 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (24848) covalent geometry : angle 0.61421 / 0.33 (33720) SS BOND : bond 0.01195 / 0.70 ( 8) SS BOND : angle 0.93456 / 0.52 ( 16) hydrogen bonds : bond 0.06679 / 4.53 ( 983) hydrogen bonds : angle 3.83967 / 2.75 ( 2685) metal coordination : bond 0.00683 / 0.45 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 339 time to evaluate : 0.923 Fit side-chains REVERT: A 52 ARG cc_start: 0.7394 (mtm180) cc_final: 0.6814 (mpt-90) REVERT: A 270 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8395 (mm-30) REVERT: B 270 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8373 (mm-30) REVERT: C 270 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: D 270 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: E 44 LEU cc_start: 0.8553 (mp) cc_final: 0.8241 (mm) REVERT: E 173 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6039 (ttm170) REVERT: E 404 ASN cc_start: 0.8619 (t0) cc_final: 0.8401 (t0) REVERT: E 414 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7741 (t70) REVERT: F 44 LEU cc_start: 0.8539 (mp) cc_final: 0.8215 (mm) REVERT: F 131 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: F 173 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6102 (ttm170) REVERT: F 404 ASN cc_start: 0.8609 (t0) cc_final: 0.8394 (t0) REVERT: F 414 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7758 (t70) REVERT: G 44 LEU cc_start: 0.8550 (mp) cc_final: 0.8229 (mm) REVERT: G 173 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6070 (ttm170) REVERT: G 404 ASN cc_start: 0.8584 (t0) cc_final: 0.8381 (t0) REVERT: G 414 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7737 (t70) REVERT: H 44 LEU cc_start: 0.8542 (mp) cc_final: 0.8227 (mm) REVERT: H 173 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6095 (ttm170) REVERT: H 414 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7779 (t70) outliers start: 100 outliers final: 39 residues processed: 405 average time/residue: 0.6937 time to fit residues: 319.3448 Evaluate side-chains 383 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 289 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN D 404 ASN E 53 GLN E 93 GLN F 53 GLN F 93 GLN G 53 GLN G 93 GLN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111167 restraints weight = 24131.878| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.63 r_work: 0.3205 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24888 Z= 0.088 Angle : 0.442 5.112 33736 Z= 0.234 Chirality : 0.043 0.224 3688 Planarity : 0.004 0.043 4488 Dihedral : 5.716 57.983 3675 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.02 % Allowed : 15.98 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3136 helix: 1.15 (0.15), residues: 1264 sheet: 0.31 (0.25), residues: 472 loop : -0.76 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 201 TYR 0.007 0.001 TYR C 333 PHE 0.012 0.001 PHE H 294 TRP 0.003 0.000 TRP G 289 HIS 0.003 0.000 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (24848) covalent geometry : angle 0.44201 / 0.23 (33720) SS BOND : bond 0.00563 / 0.33 ( 8) SS BOND : angle 0.99048 / 0.54 ( 16) hydrogen bonds : bond 0.03616 / 2.46 ( 983) hydrogen bonds : angle 3.48513 / 2.49 ( 2685) metal coordination : bond 0.00101 / 0.06 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 337 time to evaluate : 0.916 Fit side-chains REVERT: A 52 ARG cc_start: 0.7434 (mtm180) cc_final: 0.6889 (mpt-90) REVERT: A 53 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: A 173 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.5640 (ttm-80) REVERT: B 53 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: B 173 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.5638 (ttm-80) REVERT: C 53 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7746 (mt0) REVERT: C 173 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.5610 (ttm-80) REVERT: D 53 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: D 173 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5610 (ttm-80) REVERT: E 173 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.5513 (ttm-80) REVERT: E 404 ASN cc_start: 0.8425 (t0) cc_final: 0.8183 (t0) REVERT: E 414 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7651 (t70) REVERT: F 173 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.5530 (ttm-80) REVERT: F 404 ASN cc_start: 0.8420 (t0) cc_final: 0.8189 (t0) REVERT: F 414 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7651 (t70) REVERT: G 173 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.5506 (ttm-80) REVERT: G 404 ASN cc_start: 0.8363 (t0) cc_final: 0.8128 (t0) REVERT: G 414 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7644 (t70) REVERT: H 173 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6108 (ttm170) REVERT: H 414 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7652 (t70) outliers start: 73 outliers final: 24 residues processed: 381 average time/residue: 0.6686 time to fit residues: 292.0573 Evaluate side-chains 362 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 199 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN C 26 GLN D 26 GLN D 53 GLN E 26 GLN E 53 GLN F 26 GLN F 53 GLN G 26 GLN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104433 restraints weight = 24047.115| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.60 r_work: 0.3106 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 24888 Z= 0.270 Angle : 0.646 9.064 33736 Z= 0.349 Chirality : 0.051 0.228 3688 Planarity : 0.006 0.051 4488 Dihedral : 6.837 56.235 3659 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.93 % Allowed : 14.78 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3136 helix: 0.77 (0.14), residues: 1264 sheet: 0.26 (0.25), residues: 472 loop : -1.00 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 247 TYR 0.017 0.003 TYR C 333 PHE 0.018 0.003 PHE E 294 TRP 0.009 0.002 TRP G 289 HIS 0.004 0.001 HIS H 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.27 (24848) covalent geometry : angle 0.64521 / 0.35 (33720) SS BOND : bond 0.01329 / 0.78 ( 8) SS BOND : angle 1.22462 / 0.75 ( 16) hydrogen bonds : bond 0.06997 / 4.73 ( 983) hydrogen bonds : angle 3.78339 / 2.71 ( 2685) metal coordination : bond 0.00728 / 0.47 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 325 time to evaluate : 1.052 Fit side-chains REVERT: A 37 GLN cc_start: 0.7217 (mm110) cc_final: 0.6809 (mp-120) REVERT: A 52 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6794 (mpt-90) REVERT: A 53 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: A 173 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.5735 (ttm-80) REVERT: B 173 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5765 (ttm-80) REVERT: C 37 GLN cc_start: 0.7217 (mm110) cc_final: 0.6810 (mp-120) REVERT: C 173 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.5766 (ttm-80) REVERT: D 173 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.5743 (ttm-80) REVERT: E 404 ASN cc_start: 0.8572 (t0) cc_final: 0.8354 (t0) REVERT: E 414 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7735 (t70) REVERT: F 404 ASN cc_start: 0.8559 (t0) cc_final: 0.8339 (t0) REVERT: F 414 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7756 (t70) REVERT: G 404 ASN cc_start: 0.8550 (t0) cc_final: 0.8311 (t0) REVERT: G 414 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7744 (t70) REVERT: H 37 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6333 (tt0) REVERT: H 414 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7778 (t70) outliers start: 95 outliers final: 54 residues processed: 395 average time/residue: 0.6993 time to fit residues: 315.3556 Evaluate side-chains 377 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 209 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 220 optimal weight: 0.2980 chunk 119 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN D 404 ASN E 53 GLN F 53 GLN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109565 restraints weight = 24304.729| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.64 r_work: 0.3177 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24888 Z= 0.100 Angle : 0.459 5.496 33736 Z= 0.244 Chirality : 0.043 0.225 3688 Planarity : 0.005 0.043 4488 Dihedral : 5.482 54.509 3659 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 15.60 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3136 helix: 1.13 (0.15), residues: 1264 sheet: 0.31 (0.24), residues: 472 loop : -0.83 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 52 TYR 0.008 0.001 TYR A 333 PHE 0.012 0.001 PHE H 294 TRP 0.004 0.001 TRP F 289 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (24848) covalent geometry : angle 0.45871 / 0.24 (33720) SS BOND : bond 0.00605 / 0.36 ( 8) SS BOND : angle 1.00408 / 0.57 ( 16) hydrogen bonds : bond 0.04011 / 2.73 ( 983) hydrogen bonds : angle 3.48600 / 2.50 ( 2685) metal coordination : bond 0.00204 / 0.13 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 323 time to evaluate : 0.914 Fit side-chains REVERT: A 173 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.5640 (ttm-80) REVERT: B 53 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: B 173 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.5638 (ttm-80) REVERT: C 53 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: C 173 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.5646 (ttm-80) REVERT: D 53 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: D 173 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5625 (ttm-80) REVERT: E 55 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6727 (mt) REVERT: E 173 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.5861 (ttm170) REVERT: E 414 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7661 (t70) REVERT: F 55 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6769 (mt) REVERT: F 173 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.5912 (ttm170) REVERT: F 414 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7669 (t70) REVERT: G 173 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.5881 (ttm170) REVERT: G 404 ASN cc_start: 0.8323 (t0) cc_final: 0.8110 (t0) REVERT: G 414 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7651 (t70) REVERT: H 55 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6846 (mt) REVERT: H 173 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.5893 (ttm170) REVERT: H 414 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7670 (t70) outliers start: 69 outliers final: 36 residues processed: 373 average time/residue: 0.6517 time to fit residues: 280.0671 Evaluate side-chains 373 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 319 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 298 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 307 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 311 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 278 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN H 53 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110908 restraints weight = 24096.959| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.62 r_work: 0.3203 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24888 Z= 0.091 Angle : 0.439 4.749 33736 Z= 0.232 Chirality : 0.043 0.220 3688 Planarity : 0.004 0.040 4488 Dihedral : 5.109 52.968 3656 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 16.97 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3136 helix: 1.66 (0.15), residues: 1208 sheet: 0.39 (0.26), residues: 432 loop : -0.78 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 52 TYR 0.007 0.001 TYR C 333 PHE 0.012 0.001 PHE G 294 TRP 0.003 0.001 TRP E 289 HIS 0.005 0.000 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (24848) covalent geometry : angle 0.43828 / 0.23 (33720) SS BOND : bond 0.00521 / 0.31 ( 8) SS BOND : angle 1.01937 / 0.57 ( 16) hydrogen bonds : bond 0.03646 / 2.48 ( 983) hydrogen bonds : angle 3.40039 / 2.44 ( 2685) metal coordination : bond 0.00187 / 0.12 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 323 time to evaluate : 0.937 Fit side-chains REVERT: A 173 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.5647 (ttm-80) REVERT: A 313 VAL cc_start: 0.5954 (OUTLIER) cc_final: 0.5707 (p) REVERT: B 53 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: B 173 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5647 (ttm-80) REVERT: B 313 VAL cc_start: 0.5980 (OUTLIER) cc_final: 0.5735 (p) REVERT: B 385 ASP cc_start: 0.8096 (p0) cc_final: 0.7890 (p0) REVERT: C 53 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: C 173 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5645 (ttm-80) REVERT: C 313 VAL cc_start: 0.5961 (OUTLIER) cc_final: 0.5713 (p) REVERT: C 385 ASP cc_start: 0.8085 (p0) cc_final: 0.7876 (p0) REVERT: D 53 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: D 173 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.5641 (ttm-80) REVERT: D 313 VAL cc_start: 0.5956 (OUTLIER) cc_final: 0.5711 (p) REVERT: E 173 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5843 (ttm170) REVERT: E 327 GLN cc_start: 0.6967 (mp10) cc_final: 0.6585 (mm-40) REVERT: E 391 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: E 414 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7632 (t70) REVERT: F 173 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.5859 (ttm170) REVERT: F 327 GLN cc_start: 0.6975 (mp10) cc_final: 0.6591 (mm-40) REVERT: F 414 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7630 (t70) REVERT: G 173 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.5841 (ttm170) REVERT: G 327 GLN cc_start: 0.6991 (mp10) cc_final: 0.6629 (mm-40) REVERT: G 414 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7618 (t70) REVERT: H 414 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7638 (t70) outliers start: 58 outliers final: 27 residues processed: 363 average time/residue: 0.7148 time to fit residues: 295.5873 Evaluate side-chains 354 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 391 GLU Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 0.0970 chunk 242 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 285 GLN A 404 ASN B 26 GLN B 53 GLN B 285 GLN B 404 ASN C 26 GLN C 53 GLN C 285 GLN C 404 ASN D 26 GLN D 53 GLN D 285 GLN D 404 ASN E 26 GLN E 53 GLN F 26 GLN F 53 GLN G 26 GLN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105522 restraints weight = 24016.851| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.61 r_work: 0.3125 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24888 Z= 0.206 Angle : 0.579 8.336 33736 Z= 0.311 Chirality : 0.048 0.225 3688 Planarity : 0.005 0.047 4488 Dihedral : 6.359 56.510 3656 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.77 % Allowed : 17.51 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3136 helix: 1.07 (0.15), residues: 1264 sheet: 0.44 (0.25), residues: 472 loop : -0.96 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 315 TYR 0.015 0.002 TYR A 333 PHE 0.017 0.002 PHE H 294 TRP 0.007 0.001 TRP F 289 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (24848) covalent geometry : angle 0.57826 / 0.31 (33720) SS BOND : bond 0.01032 / 0.60 ( 8) SS BOND : angle 1.17651 / 0.71 ( 16) hydrogen bonds : bond 0.06145 / 4.16 ( 983) hydrogen bonds : angle 3.66774 / 2.63 ( 2685) metal coordination : bond 0.00555 / 0.37 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 314 time to evaluate : 0.939 Fit side-chains REVERT: A 52 ARG cc_start: 0.7612 (mtm180) cc_final: 0.6726 (mpt-90) REVERT: A 173 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5657 (ttm-80) REVERT: B 173 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.5655 (ttm-80) REVERT: C 173 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.5678 (ttm-80) REVERT: D 173 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.5646 (ttm-80) REVERT: E 173 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6003 (ttm170) REVERT: E 313 VAL cc_start: 0.5624 (OUTLIER) cc_final: 0.5175 (p) REVERT: E 414 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7740 (t70) REVERT: F 173 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6065 (ttm170) REVERT: F 313 VAL cc_start: 0.5631 (OUTLIER) cc_final: 0.5179 (p) REVERT: F 414 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7729 (t70) REVERT: G 173 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6026 (ttm170) REVERT: G 313 VAL cc_start: 0.5612 (OUTLIER) cc_final: 0.5156 (p) REVERT: G 414 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7730 (t70) REVERT: H 313 VAL cc_start: 0.5626 (OUTLIER) cc_final: 0.5181 (p) REVERT: H 414 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7751 (t70) outliers start: 67 outliers final: 37 residues processed: 359 average time/residue: 0.6634 time to fit residues: 274.0022 Evaluate side-chains 358 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 66 optimal weight: 0.4980 chunk 186 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 0.0040 chunk 271 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN E 53 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107837 restraints weight = 24095.210| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.61 r_work: 0.3156 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24888 Z= 0.131 Angle : 0.497 6.798 33736 Z= 0.265 Chirality : 0.045 0.224 3688 Planarity : 0.005 0.042 4488 Dihedral : 5.749 54.953 3656 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.61 % Allowed : 16.93 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3136 helix: 1.21 (0.15), residues: 1264 sheet: 0.43 (0.24), residues: 472 loop : -0.92 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.011 0.001 TYR C 333 PHE 0.014 0.002 PHE H 294 TRP 0.005 0.001 TRP F 289 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (24848) covalent geometry : angle 0.49681 / 0.26 (33720) SS BOND : bond 0.00726 / 0.42 ( 8) SS BOND : angle 1.02541 / 0.59 ( 16) hydrogen bonds : bond 0.04769 / 3.24 ( 983) hydrogen bonds : angle 3.54584 / 2.54 ( 2685) metal coordination : bond 0.00322 / 0.21 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 316 time to evaluate : 0.902 Fit side-chains REVERT: A 52 ARG cc_start: 0.7638 (mtm180) cc_final: 0.6752 (mpt-90) REVERT: A 173 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.5678 (ttm-80) REVERT: B 53 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: B 173 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.5688 (ttm-80) REVERT: C 53 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: C 173 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.5708 (ttm-80) REVERT: D 53 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: D 173 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.5677 (ttm-80) REVERT: E 173 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.5943 (ttm170) REVERT: E 414 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7720 (t70) REVERT: F 173 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6002 (ttm170) REVERT: F 414 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7658 (t70) REVERT: G 173 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5972 (ttm170) REVERT: G 414 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7666 (t70) REVERT: H 414 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7681 (t70) outliers start: 63 outliers final: 44 residues processed: 363 average time/residue: 0.6299 time to fit residues: 263.4732 Evaluate side-chains 368 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 53 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 299 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 298 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN E 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN H 26 GLN H 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106934 restraints weight = 23868.005| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24888 Z= 0.150 Angle : 0.520 6.756 33736 Z= 0.278 Chirality : 0.046 0.224 3688 Planarity : 0.005 0.043 4488 Dihedral : 5.918 55.319 3656 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.61 % Allowed : 16.72 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3136 helix: 1.20 (0.15), residues: 1264 sheet: 0.43 (0.25), residues: 472 loop : -0.96 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.012 0.002 TYR A 333 PHE 0.014 0.002 PHE H 294 TRP 0.006 0.001 TRP F 289 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (24848) covalent geometry : angle 0.51915 / 0.28 (33720) SS BOND : bond 0.00807 / 0.47 ( 8) SS BOND : angle 1.05295 / 0.62 ( 16) hydrogen bonds : bond 0.05166 / 3.50 ( 983) hydrogen bonds : angle 3.57573 / 2.56 ( 2685) metal coordination : bond 0.00369 / 0.24 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 0.906 Fit side-chains REVERT: A 52 ARG cc_start: 0.7626 (mtm180) cc_final: 0.6734 (mpt-90) REVERT: A 173 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.5665 (ttm-80) REVERT: B 173 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.5678 (ttm-80) REVERT: C 173 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.5699 (ttm-80) REVERT: D 173 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.5657 (ttm-80) REVERT: E 173 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.5908 (ttm170) REVERT: E 414 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7730 (t70) REVERT: F 173 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.5976 (ttm170) REVERT: F 414 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7711 (t70) REVERT: G 173 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.5947 (ttm170) REVERT: G 414 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7706 (t70) REVERT: H 414 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7717 (t70) outliers start: 63 outliers final: 46 residues processed: 358 average time/residue: 0.6384 time to fit residues: 263.7084 Evaluate side-chains 361 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 304 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 75 CYS Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 414 ASP Chi-restraints excluded: chain H residue 75 CYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 216 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 186 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 GLN B 26 GLN B 53 GLN B 285 GLN C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN E 26 GLN E 404 ASN F 26 GLN F 404 ASN G 53 GLN H 26 GLN H 53 GLN H 404 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105688 restraints weight = 24142.904| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.61 r_work: 0.3143 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24888 Z= 0.167 Angle : 0.540 7.583 33736 Z= 0.289 Chirality : 0.047 0.225 3688 Planarity : 0.005 0.044 4488 Dihedral : 6.102 55.707 3656 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 16.85 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3136 helix: 1.16 (0.15), residues: 1264 sheet: 0.41 (0.24), residues: 472 loop : -1.00 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.013 0.002 TYR D 333 PHE 0.015 0.002 PHE H 294 TRP 0.006 0.001 TRP H 289 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (24848) covalent geometry : angle 0.53936 / 0.29 (33720) SS BOND : bond 0.00883 / 0.52 ( 8) SS BOND : angle 1.07937 / 0.64 ( 16) hydrogen bonds : bond 0.05502 / 3.73 ( 983) hydrogen bonds : angle 3.60550 / 2.58 ( 2685) metal coordination : bond 0.00425 / 0.28 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9133.21 seconds wall clock time: 156 minutes 6.13 seconds (9366.13 seconds total)