Starting phenix.real_space_refine on Fri May 23 17:40:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_35454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_35454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_35454.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_35454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihs_35454/05_2025/8ihs_35454.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.58, per 1000 atoms: 0.56 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: 6.82 Conformation dependent library (CDL) restraints added in 3.8 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: 3.13 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: 8.00 Time building geometry restraints manager: 7.74 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 - 17.83: 12769 17.83 - 35.65: 1457 35.65 - 53.48: 424 53.48 - 71.30: 77 71.30 - 89.12: 73 Dihedral angle restraints: 14800 sinusoidal: 5840 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 14797 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.920 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 17.351 89.125 9096 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 3.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.004 0.001 TRP H 79 HIS 0.011 0.001 HIS G 251 PHE 0.013 0.002 PHE H 294 TYR 0.011 0.001 TYR C 333 ARG 0.008 0.000 ARG H 315 Details of bonding type rmsd hydrogen bonds : bond 0.16419 ( 983) hydrogen bonds : angle 5.09486 ( 2685) metal coordination : bond 0.18535 ( 32) SS BOND : bond 0.00852 ( 8) SS BOND : angle 2.37509 ( 16) covalent geometry : bond 0.00534 (24848) covalent geometry : angle 0.64733 (33720) *********************** 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 : 2.437 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: 0.6475 (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: 0.8386 (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: 0.6797 (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: 0.8013 (tptp) cc_final: 0.7807 (tptp) REVERT: H 174 LEU cc_start: 0.7662 (mt) cc_final: 0.7458 (mt) REVERT: H 281 ARG cc_start: 0.7375 (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: 1.4885 time to fit residues: 784.1954 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 : 2.640 ------------------------------------------------------------------------------- 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 263 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 404 ASN B 26 GLN B 53 GLN B 404 ASN C 26 GLN C 53 GLN C 404 ASN D 26 GLN D 53 GLN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104611 restraints weight = 24047.939| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.61 r_work: 0.3124 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24888 Z= 0.217 Angle : 0.610 8.836 33736 Z= 0.328 Chirality : 0.049 0.228 3688 Planarity : 0.006 0.047 4488 Dihedral : 10.461 85.891 3771 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.64 % Allowed : 16.31 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3136 helix: 0.75 (0.15), residues: 1264 sheet: -0.02 (0.25), residues: 472 loop : -0.85 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.008 0.001 HIS C 251 PHE 0.016 0.002 PHE F 294 TYR 0.016 0.002 TYR G 244 ARG 0.004 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.06591 ( 983) hydrogen bonds : angle 3.92799 ( 2685) metal coordination : bond 0.00806 ( 32) SS BOND : bond 0.01119 ( 8) SS BOND : angle 0.74937 ( 16) covalent geometry : bond 0.00511 (24848) covalent geometry : angle 0.61003 (33720) *********************** 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: 88 poor density : 342 time to evaluate : 2.734 Fit side-chains REVERT: A 52 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6829 (mpt-90) REVERT: A 270 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: B 270 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: C 270 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: D 270 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: E 44 LEU cc_start: 0.8491 (mp) cc_final: 0.8160 (mm) REVERT: E 131 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: E 172 GLU cc_start: 0.7815 (pt0) cc_final: 0.7562 (pt0) REVERT: E 173 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.5565 (ttm-80) REVERT: E 281 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7365 (mtm110) REVERT: E 414 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7788 (t70) REVERT: F 44 LEU cc_start: 0.8490 (mp) cc_final: 0.8166 (mm) REVERT: F 131 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: F 172 GLU cc_start: 0.7822 (pt0) cc_final: 0.7574 (pt0) REVERT: F 173 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6158 (ttm170) REVERT: F 281 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7355 (mtm110) REVERT: F 414 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7799 (t70) REVERT: G 44 LEU cc_start: 0.8489 (mp) cc_final: 0.8183 (mm) REVERT: G 131 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: G 172 GLU cc_start: 0.7808 (pt0) cc_final: 0.7575 (pt0) REVERT: G 173 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.5603 (ttm-80) REVERT: G 281 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7380 (mtm110) REVERT: G 414 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7782 (t70) REVERT: H 44 LEU cc_start: 0.8489 (mp) cc_final: 0.8175 (mm) REVERT: H 131 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: H 173 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.5566 (ttm-80) REVERT: H 281 ARG cc_start: 0.7762 (mtp180) cc_final: 0.7358 (mtm110) REVERT: H 414 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7808 (t70) outliers start: 88 outliers final: 39 residues processed: 401 average time/residue: 1.5512 time to fit residues: 705.1490 Evaluate side-chains 374 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain E residue 131 GLU 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 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 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 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 131 GLU 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 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 96 SER Chi-restraints excluded: chain H residue 131 GLU 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 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 28 optimal weight: 0.9990 chunk 269 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN D 404 ASN E 53 GLN E 93 GLN E 404 ASN F 53 GLN F 93 GLN F 404 ASN G 53 GLN G 93 GLN G 404 ASN H 53 GLN H 93 GLN H 404 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110663 restraints weight = 23912.985| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.61 r_work: 0.3202 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24888 Z= 0.094 Angle : 0.452 5.404 33736 Z= 0.239 Chirality : 0.043 0.225 3688 Planarity : 0.004 0.042 4488 Dihedral : 8.817 79.820 3771 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.81 % Allowed : 16.76 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3136 helix: 1.11 (0.15), residues: 1264 sheet: 0.22 (0.25), residues: 472 loop : -0.72 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 289 HIS 0.003 0.000 HIS A 251 PHE 0.013 0.001 PHE H 294 TYR 0.008 0.001 TYR A 333 ARG 0.003 0.000 ARG H 201 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 983) hydrogen bonds : angle 3.55419 ( 2685) metal coordination : bond 0.00175 ( 32) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.06239 ( 16) covalent geometry : bond 0.00200 (24848) covalent geometry : angle 0.45185 (33720) *********************** 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 412 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 2.690 Fit side-chains REVERT: A 52 ARG cc_start: 0.7406 (mtm180) cc_final: 0.6899 (mpt-90) REVERT: B 53 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: C 53 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: D 53 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: E 44 LEU cc_start: 0.8434 (mp) cc_final: 0.8166 (mm) REVERT: E 172 GLU cc_start: 0.7655 (pt0) cc_final: 0.7432 (pt0) REVERT: E 327 GLN cc_start: 0.6981 (mp-120) cc_final: 0.6616 (mm-40) REVERT: E 414 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7651 (t70) REVERT: F 44 LEU cc_start: 0.8420 (mp) cc_final: 0.8148 (mm) REVERT: F 172 GLU cc_start: 0.7688 (pt0) cc_final: 0.7439 (pt0) REVERT: F 327 GLN cc_start: 0.7002 (mp-120) cc_final: 0.6628 (mm-40) REVERT: F 414 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7652 (t70) REVERT: G 44 LEU cc_start: 0.8446 (mp) cc_final: 0.8178 (mm) REVERT: G 172 GLU cc_start: 0.7664 (pt0) cc_final: 0.7433 (pt0) REVERT: G 414 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7627 (t70) REVERT: H 44 LEU cc_start: 0.8430 (mp) cc_final: 0.8158 (mm) REVERT: H 414 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7659 (t70) outliers start: 68 outliers final: 24 residues processed: 381 average time/residue: 1.3969 time to fit residues: 609.1754 Evaluate side-chains 362 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 331 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 53 GLN 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 300 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 53 GLN 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 311 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103471 restraints weight = 24223.142| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.61 r_work: 0.3108 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 24888 Z= 0.265 Angle : 0.644 8.911 33736 Z= 0.347 Chirality : 0.051 0.227 3688 Planarity : 0.006 0.050 4488 Dihedral : 9.826 83.465 3757 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.14 % Allowed : 14.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3136 helix: 0.77 (0.14), residues: 1264 sheet: 0.23 (0.27), residues: 432 loop : -0.96 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 289 HIS 0.008 0.001 HIS A 251 PHE 0.018 0.003 PHE H 294 TYR 0.017 0.003 TYR A 333 ARG 0.005 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.06960 ( 983) hydrogen bonds : angle 3.80587 ( 2685) metal coordination : bond 0.00772 ( 32) SS BOND : bond 0.01339 ( 8) SS BOND : angle 1.08686 ( 16) covalent geometry : bond 0.00635 (24848) covalent geometry : angle 0.64369 (33720) *********************** 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 425 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 325 time to evaluate : 2.517 Fit side-chains REVERT: A 52 ARG cc_start: 0.7392 (mtm180) cc_final: 0.6801 (mpt-90) REVERT: A 270 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: B 270 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8422 (mm-30) REVERT: C 270 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: D 270 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8380 (mm-30) REVERT: E 44 LEU cc_start: 0.8561 (mp) cc_final: 0.8245 (mm) REVERT: E 172 GLU cc_start: 0.7802 (pt0) cc_final: 0.7541 (pt0) REVERT: E 173 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.5995 (ttm170) REVERT: E 270 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: E 414 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (t70) REVERT: F 44 LEU cc_start: 0.8548 (mp) cc_final: 0.8228 (mm) REVERT: F 172 GLU cc_start: 0.7793 (pt0) cc_final: 0.7539 (pt0) REVERT: F 173 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6050 (ttm170) REVERT: F 270 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8345 (mm-30) REVERT: F 414 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7760 (t70) REVERT: G 37 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6370 (tt0) REVERT: G 44 LEU cc_start: 0.8565 (mp) cc_final: 0.8245 (mm) REVERT: G 55 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6939 (mt) REVERT: G 172 GLU cc_start: 0.7795 (pt0) cc_final: 0.7533 (pt0) REVERT: G 173 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6010 (ttm170) REVERT: G 270 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8352 (mm-30) REVERT: G 414 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7763 (t70) REVERT: H 37 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6355 (tt0) REVERT: H 44 LEU cc_start: 0.8548 (mp) cc_final: 0.8229 (mm) REVERT: H 173 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6020 (ttm170) REVERT: H 270 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8352 (mm-30) REVERT: H 414 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7780 (t70) outliers start: 100 outliers final: 39 residues processed: 397 average time/residue: 1.4577 time to fit residues: 659.2878 Evaluate side-chains 379 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 A residue 376 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 B residue 326 SER Chi-restraints excluded: chain B residue 376 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 C residue 326 SER Chi-restraints excluded: chain C residue 376 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 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 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 270 GLU 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 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 270 GLU 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 55 LEU 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 270 GLU 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 270 GLU 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 20 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106305 restraints weight = 24120.659| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.62 r_work: 0.3138 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24888 Z= 0.159 Angle : 0.536 7.871 33736 Z= 0.286 Chirality : 0.046 0.227 3688 Planarity : 0.005 0.045 4488 Dihedral : 9.165 79.510 3757 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.35 % Allowed : 15.02 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3136 helix: 0.93 (0.15), residues: 1264 sheet: 0.33 (0.25), residues: 472 loop : -0.94 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.014 0.002 PHE H 294 TYR 0.012 0.002 TYR B 333 ARG 0.003 0.000 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 983) hydrogen bonds : angle 3.63760 ( 2685) metal coordination : bond 0.00409 ( 32) SS BOND : bond 0.00907 ( 8) SS BOND : angle 0.98657 ( 16) covalent geometry : bond 0.00368 (24848) covalent geometry : angle 0.53528 (33720) *********************** 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 421 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 340 time to evaluate : 2.440 Fit side-chains REVERT: A 52 ARG cc_start: 0.7399 (mtm180) cc_final: 0.6802 (mpt-90) REVERT: A 53 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: E 37 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6310 (tt0) REVERT: E 44 LEU cc_start: 0.8525 (mp) cc_final: 0.8208 (mm) REVERT: E 172 GLU cc_start: 0.7736 (pt0) cc_final: 0.7479 (pt0) REVERT: E 173 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.5450 (ttm-80) REVERT: E 414 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7728 (t70) REVERT: F 37 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6293 (tt0) REVERT: F 44 LEU cc_start: 0.8509 (mp) cc_final: 0.8196 (mm) REVERT: F 172 GLU cc_start: 0.7741 (pt0) cc_final: 0.7513 (pt0) REVERT: F 173 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.5478 (ttm-80) REVERT: F 414 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7728 (t70) REVERT: G 37 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6291 (tt0) REVERT: G 44 LEU cc_start: 0.8512 (mp) cc_final: 0.8187 (mm) REVERT: G 172 GLU cc_start: 0.7730 (pt0) cc_final: 0.7472 (pt0) REVERT: G 173 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.5452 (ttm-80) REVERT: G 414 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7715 (t70) REVERT: H 37 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6276 (tt0) REVERT: H 44 LEU cc_start: 0.8510 (mp) cc_final: 0.8198 (mm) REVERT: H 173 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6052 (ttm170) REVERT: H 414 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7742 (t70) outliers start: 81 outliers final: 42 residues processed: 396 average time/residue: 1.3843 time to fit residues: 628.3201 Evaluate side-chains 386 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 124 SER 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 124 SER 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 124 SER 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 124 SER 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 35 SER 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 35 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 244 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 53 GLN C 26 GLN C 53 GLN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 53 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 53 GLN E 93 GLN E 404 ASN F 26 GLN F 53 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 53 GLN G 93 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3633 r_free = 0.3633 target = 0.138315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103365 restraints weight = 23998.858| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.61 r_work: 0.3105 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 24888 Z= 0.269 Angle : 0.653 9.607 33736 Z= 0.352 Chirality : 0.051 0.228 3688 Planarity : 0.006 0.050 4488 Dihedral : 9.838 82.150 3757 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.22 % Allowed : 14.86 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3136 helix: 0.71 (0.14), residues: 1264 sheet: 0.45 (0.28), residues: 376 loop : -1.14 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.009 0.001 HIS A 251 PHE 0.018 0.003 PHE H 294 TYR 0.017 0.003 TYR B 333 ARG 0.005 0.001 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.07069 ( 983) hydrogen bonds : angle 3.82166 ( 2685) metal coordination : bond 0.00741 ( 32) SS BOND : bond 0.01300 ( 8) SS BOND : angle 1.26077 ( 16) covalent geometry : bond 0.00646 (24848) covalent geometry : angle 0.65250 (33720) *********************** 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 435 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 333 time to evaluate : 2.582 Fit side-chains REVERT: A 52 ARG cc_start: 0.7448 (mtm180) cc_final: 0.6766 (mpt-90) REVERT: A 53 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: A 270 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8434 (mm-30) REVERT: B 270 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: C 270 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8393 (mm-30) REVERT: D 270 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: E 37 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6467 (tt0) REVERT: E 44 LEU cc_start: 0.8562 (mp) cc_final: 0.8245 (mm) REVERT: E 173 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6035 (ttm170) REVERT: E 270 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: E 414 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7761 (t70) REVERT: F 37 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6442 (tt0) REVERT: F 44 LEU cc_start: 0.8565 (mp) cc_final: 0.8247 (mm) REVERT: F 173 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6095 (ttm170) REVERT: F 270 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: F 313 VAL cc_start: 0.5726 (OUTLIER) cc_final: 0.5245 (p) REVERT: F 414 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7776 (t70) REVERT: G 37 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6426 (tt0) REVERT: G 44 LEU cc_start: 0.8557 (mp) cc_final: 0.8211 (mm) REVERT: G 173 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6059 (ttm170) REVERT: G 270 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8363 (mm-30) REVERT: G 313 VAL cc_start: 0.5701 (OUTLIER) cc_final: 0.5226 (p) REVERT: G 414 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7776 (t70) REVERT: H 37 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6415 (tt0) REVERT: H 44 LEU cc_start: 0.8555 (mp) cc_final: 0.8218 (mm) REVERT: H 173 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6103 (ttm170) REVERT: H 270 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8364 (mm-30) REVERT: H 414 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7800 (t70) outliers start: 102 outliers final: 56 residues processed: 410 average time/residue: 1.4035 time to fit residues: 663.7404 Evaluate side-chains 404 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 2.700 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 251 HIS Chi-restraints excluded: chain E residue 270 GLU 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 251 HIS Chi-restraints excluded: chain F residue 270 GLU 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 96 SER Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 270 GLU 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 251 HIS Chi-restraints excluded: chain H residue 270 GLU 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 44 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 404 ASN F 53 GLN F 404 ASN G 53 GLN G 404 ASN 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 = 0.3693 r_free = 0.3693 target = 0.143406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109017 restraints weight = 24295.855| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.59 r_work: 0.3190 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24888 Z= 0.097 Angle : 0.460 5.509 33736 Z= 0.243 Chirality : 0.043 0.223 3688 Planarity : 0.005 0.046 4488 Dihedral : 7.827 69.536 3757 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.19 % Allowed : 16.93 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3136 helix: 1.11 (0.15), residues: 1264 sheet: 0.32 (0.25), residues: 472 loop : -0.88 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 289 HIS 0.005 0.001 HIS G 251 PHE 0.012 0.001 PHE H 294 TYR 0.007 0.001 TYR A 333 ARG 0.007 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 983) hydrogen bonds : angle 3.48643 ( 2685) metal coordination : bond 0.00128 ( 32) SS BOND : bond 0.00560 ( 8) SS BOND : angle 1.04895 ( 16) covalent geometry : bond 0.00205 (24848) covalent geometry : angle 0.45914 (33720) *********************** 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 398 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 2.742 Fit side-chains REVERT: B 53 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: C 53 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7776 (mt0) REVERT: D 53 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: E 173 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5286 (ttm-80) REVERT: E 414 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7688 (t70) REVERT: F 173 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.5329 (ttm-80) REVERT: F 414 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7676 (t70) REVERT: G 173 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.5265 (ttm-80) REVERT: G 414 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (t70) REVERT: H 44 LEU cc_start: 0.8427 (mp) cc_final: 0.8117 (mm) REVERT: H 173 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.5990 (ttm170) REVERT: H 414 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7687 (t70) outliers start: 53 outliers final: 37 residues processed: 382 average time/residue: 1.3266 time to fit residues: 583.2192 Evaluate side-chains 380 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 332 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 44 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 309 optimal weight: 0.9990 chunk 284 optimal weight: 0.3980 chunk 299 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 53 GLN C 26 GLN C 53 GLN D 26 GLN D 53 GLN E 53 GLN F 53 GLN G 53 GLN H 26 GLN H 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107826 restraints weight = 24062.588| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.61 r_work: 0.3160 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24888 Z= 0.129 Angle : 0.497 6.095 33736 Z= 0.264 Chirality : 0.045 0.220 3688 Planarity : 0.005 0.045 4488 Dihedral : 7.952 72.350 3754 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.48 % Allowed : 17.14 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3136 helix: 1.18 (0.15), residues: 1264 sheet: 0.42 (0.25), residues: 472 loop : -0.90 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 289 HIS 0.006 0.001 HIS A 251 PHE 0.013 0.002 PHE E 294 TYR 0.010 0.001 TYR B 333 ARG 0.005 0.000 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 983) hydrogen bonds : angle 3.53526 ( 2685) metal coordination : bond 0.00300 ( 32) SS BOND : bond 0.00723 ( 8) SS BOND : angle 1.05228 ( 16) covalent geometry : bond 0.00290 (24848) covalent geometry : angle 0.49615 (33720) *********************** 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 394 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 2.818 Fit side-chains REVERT: E 173 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6066 (ttm170) REVERT: E 414 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7711 (t70) REVERT: F 173 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6114 (ttm170) REVERT: F 313 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5203 (p) REVERT: F 414 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7705 (t70) REVERT: G 26 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: G 173 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6082 (ttm170) REVERT: G 313 VAL cc_start: 0.5646 (OUTLIER) cc_final: 0.5193 (p) REVERT: G 414 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7702 (t70) REVERT: H 55 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6771 (mt) REVERT: H 173 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.5505 (ttm-80) REVERT: H 313 VAL cc_start: 0.5581 (OUTLIER) cc_final: 0.5147 (p) REVERT: H 414 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7723 (t70) outliers start: 60 outliers final: 38 residues processed: 376 average time/residue: 1.3266 time to fit residues: 574.2475 Evaluate side-chains 378 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER 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 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 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 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 26 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 21 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 214 optimal weight: 0.0470 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 162 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 overall best weight: 3.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 285 GLN A 404 ASN B 26 GLN B 53 GLN B 285 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 53 GLN C 285 GLN D 26 GLN D 53 GLN D 285 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN E 53 GLN ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN F 53 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 53 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN H 53 GLN ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104678 restraints weight = 24121.237| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.61 r_work: 0.3123 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24888 Z= 0.203 Angle : 0.584 8.395 33736 Z= 0.313 Chirality : 0.048 0.225 3688 Planarity : 0.005 0.048 4488 Dihedral : 9.218 79.020 3754 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.90 % Allowed : 16.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3136 helix: 0.99 (0.15), residues: 1264 sheet: 0.39 (0.25), residues: 472 loop : -1.02 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 289 HIS 0.008 0.001 HIS A 251 PHE 0.016 0.002 PHE H 294 TYR 0.014 0.002 TYR C 333 ARG 0.004 0.001 ARG D 315 Details of bonding type rmsd hydrogen bonds : bond 0.06088 ( 983) hydrogen bonds : angle 3.69344 ( 2685) metal coordination : bond 0.00531 ( 32) SS BOND : bond 0.01012 ( 8) SS BOND : angle 1.17375 ( 16) covalent geometry : bond 0.00480 (24848) covalent geometry : angle 0.58316 (33720) *********************** 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 392 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 322 time to evaluate : 2.851 Fit side-chains REVERT: A 52 ARG cc_start: 0.7642 (mtm180) cc_final: 0.6743 (mpt-90) REVERT: E 173 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.5469 (ttm-80) REVERT: E 313 VAL cc_start: 0.5660 (OUTLIER) cc_final: 0.5209 (p) REVERT: E 414 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7736 (t70) REVERT: F 173 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.5521 (ttm-80) REVERT: F 313 VAL cc_start: 0.5672 (OUTLIER) cc_final: 0.5216 (p) REVERT: F 414 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7736 (t70) REVERT: G 173 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.5474 (ttm-80) REVERT: G 313 VAL cc_start: 0.5739 (OUTLIER) cc_final: 0.5280 (p) REVERT: G 414 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7734 (t70) REVERT: H 173 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.5568 (ttm-80) REVERT: H 313 VAL cc_start: 0.5719 (OUTLIER) cc_final: 0.5269 (p) REVERT: H 414 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7754 (t70) outliers start: 70 outliers final: 45 residues processed: 374 average time/residue: 1.3355 time to fit residues: 578.2581 Evaluate side-chains 376 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 2.436 ------------------------------------------------------------------------------- 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 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 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 124 SER 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 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 94 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 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 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 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 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 173 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 0.4980 chunk 308 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 226 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 288 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN 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 53 GLN ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111208 restraints weight = 24213.244| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.63 r_work: 0.3207 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1712 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 : 0.449 6.012 33736 Z= 0.237 Chirality : 0.043 0.217 3688 Planarity : 0.004 0.043 4488 Dihedral : 7.078 62.144 3754 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.32 % Allowed : 17.43 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3136 helix: 1.60 (0.15), residues: 1208 sheet: 0.38 (0.26), residues: 432 loop : -0.87 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 289 HIS 0.005 0.000 HIS F 251 PHE 0.012 0.001 PHE H 294 TYR 0.007 0.001 TYR B 333 ARG 0.004 0.000 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 983) hydrogen bonds : angle 3.43716 ( 2685) metal coordination : bond 0.00117 ( 32) SS BOND : bond 0.00482 ( 8) SS BOND : angle 1.09362 ( 16) covalent geometry : bond 0.00193 (24848) covalent geometry : angle 0.44861 (33720) ********************** 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 380 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 324 time to evaluate : 2.465 Fit side-chains REVERT: A 52 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6765 (mpt-90) REVERT: B 53 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: C 37 GLN cc_start: 0.7051 (mm110) cc_final: 0.6848 (mp10) REVERT: C 53 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: D 53 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: E 327 GLN cc_start: 0.6957 (mp10) cc_final: 0.6580 (mm-40) REVERT: E 414 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7676 (t70) REVERT: F 327 GLN cc_start: 0.6964 (mp10) cc_final: 0.6585 (mm-40) REVERT: F 414 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7671 (t70) REVERT: G 414 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7664 (t70) REVERT: H 313 VAL cc_start: 0.5584 (OUTLIER) cc_final: 0.5149 (p) REVERT: H 414 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7672 (t70) outliers start: 56 outliers final: 40 residues processed: 368 average time/residue: 1.3969 time to fit residues: 589.3483 Evaluate side-chains 354 residues out of total 2416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER 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 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 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 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 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 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 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 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 156 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 53 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN H 53 GLN ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105169 restraints weight = 23989.891| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.61 r_work: 0.3134 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24888 Z= 0.183 Angle : 0.558 7.486 33736 Z= 0.299 Chirality : 0.047 0.223 3688 Planarity : 0.005 0.046 4488 Dihedral : 8.667 77.911 3752 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.24 % Allowed : 17.96 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3136 helix: 1.15 (0.15), residues: 1264 sheet: 0.46 (0.24), residues: 472 loop : -0.98 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 289 HIS 0.003 0.001 HIS E 251 PHE 0.015 0.002 PHE G 294 TYR 0.013 0.002 TYR D 333 ARG 0.005 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05820 ( 983) hydrogen bonds : angle 3.61043 ( 2685) metal coordination : bond 0.00461 ( 32) SS BOND : bond 0.00918 ( 8) SS BOND : angle 1.12283 ( 16) covalent geometry : bond 0.00430 (24848) covalent geometry : angle 0.55717 (33720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18790.60 seconds wall clock time: 323 minutes 3.21 seconds (19383.21 seconds total)