Starting phenix.real_space_refine on Tue Sep 15 15:31:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.cif" model { file = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bjc_7101/09_2026/6bjc_7101.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.016 sd= 0.932 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 P 36 5.49 5 Mg 12 5.21 5 S 284 5.16 5 C 25854 2.51 5 N 7020 2.21 5 O 7930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41136 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.40, per 1000 atoms: 0.20 Number of scatterers: 41136 At special positions: 0 Unit cell: (172.9, 89.11, 214.13, 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) S 284 16.00 P 36 15.00 Mg 12 11.99 O 7930 8.00 N 7020 7.00 C 25854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 seconds 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 30 sheets defined 56.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.589A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.100A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.863A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.440A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.725A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.702A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.566A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.636A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.986A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.353A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.333A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.382A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.801A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.745A pdb=" N GLN B 281 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.687A pdb=" N ASP B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.105A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.978A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.589A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 162 removed outlier: 4.100A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.861A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.440A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.725A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.702A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.566A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.636A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.986A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.352A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.333A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.383A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.801A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.745A pdb=" N GLN D 281 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.686A pdb=" N ASP D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 400 Processing helix chain 'D' and resid 404 through 411 removed outlier: 4.105A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 437 removed outlier: 3.979A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 337 removed outlier: 3.509A pdb=" N HIS T 335 " --> pdb=" O VAL T 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.588A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 162 removed outlier: 4.100A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.862A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.441A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.724A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.702A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.567A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.635A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.986A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.353A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.332A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.746A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.381A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.562A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.801A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.746A pdb=" N GLN F 281 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.689A pdb=" N ASP F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 Processing helix chain 'F' and resid 404 through 411 removed outlier: 4.104A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 437 removed outlier: 3.978A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.588A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 162 removed outlier: 4.099A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 198 removed outlier: 3.863A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.442A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 277 through 284 removed outlier: 3.725A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.702A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.565A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.636A pdb=" N TRP J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.985A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.351A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.331A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.383A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.561A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 3.799A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.745A pdb=" N GLN H 281 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN H 282 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 282' Processing helix chain 'H' and resid 287 through 297 removed outlier: 3.687A pdb=" N ASP H 297 " --> pdb=" O GLN H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 400 Processing helix chain 'H' and resid 404 through 411 removed outlier: 4.104A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 437 removed outlier: 3.978A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.589A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 162 removed outlier: 4.101A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 198 removed outlier: 3.863A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.441A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 277 through 284 removed outlier: 3.725A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU L 284 " --> pdb=" O LYS L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.702A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 removed outlier: 3.564A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.635A pdb=" N TRP L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.985A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.350A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.332A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.383A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.799A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 278 through 282 removed outlier: 3.745A pdb=" N GLN G 281 " --> pdb=" O ARG G 278 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN G 282 " --> pdb=" O GLY G 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 278 through 282' Processing helix chain 'G' and resid 287 through 297 removed outlier: 3.687A pdb=" N ASP G 297 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 400 Processing helix chain 'G' and resid 404 through 411 removed outlier: 4.104A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 437 removed outlier: 3.978A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.613A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.589A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 removed outlier: 3.863A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.442A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 277 through 284 removed outlier: 3.725A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU K 284 " --> pdb=" O LYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.701A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.566A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.636A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.985A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.912A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.350A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 71 through 81 removed outlier: 4.333A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.383A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.560A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.799A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 278 through 282 removed outlier: 3.746A pdb=" N GLN I 281 " --> pdb=" O ARG I 278 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN I 282 " --> pdb=" O GLY I 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 278 through 282' Processing helix chain 'I' and resid 287 through 297 removed outlier: 3.687A pdb=" N ASP I 297 " --> pdb=" O GLN I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 400 Processing helix chain 'I' and resid 404 through 411 removed outlier: 4.104A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 437 removed outlier: 3.978A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 326 through 337 removed outlier: 3.505A pdb=" N HIS P 335 " --> pdb=" O VAL P 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.058A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER D 374 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE D 319 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 376 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA D 317 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE D 378 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASN D 380 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU F 3 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY F 134 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER F 140 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.295A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.056A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.296A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.058A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.623A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLU G 3 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY G 134 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER G 140 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.293A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.985A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.057A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.624A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.886A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU I 3 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY I 134 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER I 140 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.294A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.986A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) 2119 hydrogen bonds defined for protein. 6123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.95 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6979 1.32 - 1.44: 11347 1.44 - 1.56: 23219 1.56 - 1.69: 67 1.69 - 1.81: 458 Bond restraints: 42070 Sorted by residual: bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.607 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 42065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 54530 3.13 - 6.25: 2426 6.25 - 9.38: 155 9.38 - 12.50: 45 12.50 - 15.63: 6 Bond angle restraints: 57162 Sorted by residual: angle pdb=" CA THR I 109 " pdb=" C THR I 109 " pdb=" N GLU I 110 " ideal model delta sigma weight residual 119.46 116.25 3.21 6.10e-01 2.69e+00 2.77e+01 angle pdb=" C ILE A 110 " pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta sigma weight residual 119.98 125.81 -5.83 1.11e+00 8.12e-01 2.76e+01 angle pdb=" N SER D 97 " pdb=" CA SER D 97 " pdb=" C SER D 97 " ideal model delta sigma weight residual 111.40 117.80 -6.40 1.22e+00 6.72e-01 2.75e+01 angle pdb=" N SER F 97 " pdb=" CA SER F 97 " pdb=" C SER F 97 " ideal model delta sigma weight residual 111.40 117.78 -6.38 1.22e+00 6.72e-01 2.74e+01 angle pdb=" C ILE C 110 " pdb=" N GLY C 111 " pdb=" CA GLY C 111 " ideal model delta sigma weight residual 119.98 125.78 -5.80 1.11e+00 8.12e-01 2.73e+01 ... (remaining 57157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.64: 24085 33.64 - 67.28: 809 67.28 - 100.92: 42 100.92 - 134.56: 0 134.56 - 168.20: 18 Dihedral angle restraints: 24954 sinusoidal: 9918 harmonic: 15036 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.53 -168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.64 -168.09 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.92 -167.81 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4525 0.086 - 0.171: 1341 0.171 - 0.257: 307 0.257 - 0.342: 75 0.342 - 0.428: 4 Chirality restraints: 6252 Sorted by residual: chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C3' G2P B 501 " pdb=" C2' G2P B 501 " pdb=" C4' G2P B 501 " pdb=" O3' G2P B 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C3' G2P I 501 " pdb=" C2' G2P I 501 " pdb=" C4' G2P I 501 " pdb=" O3' G2P I 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 6249 not shown) Planarity restraints: 7436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.029 2.00e-02 2.50e+03 1.33e-02 5.27e+00 pdb=" C2 GTP L 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.005 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.008 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.032 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.027 2.00e-02 2.50e+03 1.25e-02 4.71e+00 pdb=" C2 GTP C 501 " -0.007 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.003 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.008 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.005 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.031 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP K 501 " -0.026 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" C2 GTP K 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GTP K 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GTP K 501 " -0.005 2.00e-02 2.50e+03 pdb=" C8 GTP K 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 GTP K 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 GTP K 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GTP K 501 " 0.006 2.00e-02 2.50e+03 pdb=" N7 GTP K 501 " 0.002 2.00e-02 2.50e+03 pdb=" N9 GTP K 501 " 0.031 2.00e-02 2.50e+03 pdb=" O6 GTP K 501 " -0.004 2.00e-02 2.50e+03 ... (remaining 7433 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 105 2.58 - 3.16: 32831 3.16 - 3.74: 66328 3.74 - 4.32: 92557 4.32 - 4.90: 155485 Nonbonded interactions: 347306 Sorted by model distance: nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.999 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.021 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 2.068 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.070 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.093 2.170 ... (remaining 347301 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'L' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'T' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.960 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 0.109 42070 Z= 0.639 Angle : 1.541 15.626 57162 Z= 1.040 Chirality : 0.087 0.428 6252 Planarity : 0.007 0.054 7436 Dihedral : 16.352 168.196 15306 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 8.25 % Favored : 88.75 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.11), residues: 5160 helix: 0.69 (0.09), residues: 2356 sheet: 0.57 (0.19), residues: 792 loop : -1.21 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 2 TYR 0.025 0.003 TYR J 224 PHE 0.022 0.003 PHE B 92 TRP 0.028 0.004 TRP L 21 HIS 0.009 0.002 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00915 / 0.64 (42070) covalent geometry : angle 1.54103 / 1.04 (57162) hydrogen bonds : bond 0.19333 / 13.34 ( 2119) hydrogen bonds : angle 7.24070 / 5.26 ( 6123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1967 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1835 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.5306 (t0) REVERT: A 178 SER cc_start: 0.8077 (p) cc_final: 0.7611 (t) REVERT: B 55 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6352 (tm-30) REVERT: B 116 ASP cc_start: 0.6632 (p0) cc_final: 0.6188 (p0) REVERT: B 325 MET cc_start: 0.6467 (mmm) cc_final: 0.6117 (mmm) REVERT: B 335 VAL cc_start: 0.8989 (t) cc_final: 0.8755 (t) REVERT: B 425 MET cc_start: 0.7631 (ttp) cc_final: 0.7405 (ttp) REVERT: C 178 SER cc_start: 0.7946 (p) cc_final: 0.7639 (p) REVERT: C 209 ILE cc_start: 0.8792 (mm) cc_final: 0.8293 (mm) REVERT: C 259 LEU cc_start: 0.8684 (tp) cc_final: 0.8477 (tp) REVERT: D 199 ASP cc_start: 0.7172 (m-30) cc_final: 0.6959 (m-30) REVERT: D 300 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7661 (t0) REVERT: D 398 MET cc_start: 0.7232 (mtt) cc_final: 0.6700 (mtt) REVERT: E 47 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.5519 (t0) REVERT: E 118 VAL cc_start: 0.8816 (m) cc_final: 0.8420 (p) REVERT: E 122 ILE cc_start: 0.8746 (mt) cc_final: 0.8513 (mt) REVERT: E 285 GLN cc_start: 0.7285 (tt0) cc_final: 0.6496 (tt0) REVERT: F 1 MET cc_start: 0.7597 (mmt) cc_final: 0.7285 (tpp) REVERT: F 163 ASP cc_start: 0.7103 (p0) cc_final: 0.6543 (p0) REVERT: F 209 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (mt) REVERT: F 257 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8004 (p) REVERT: H 55 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6733 (tm-30) REVERT: H 114 LEU cc_start: 0.8684 (tp) cc_final: 0.8484 (tp) REVERT: H 180 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8179 (m) REVERT: H 252 LEU cc_start: 0.8455 (mt) cc_final: 0.8245 (mt) REVERT: H 428 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9037 (tp) REVERT: L 328 VAL cc_start: 0.8542 (t) cc_final: 0.8323 (t) REVERT: G 114 LEU cc_start: 0.8669 (tp) cc_final: 0.8275 (tp) REVERT: G 170 SER cc_start: 0.8755 (m) cc_final: 0.8518 (p) REVERT: G 300 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 389 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8359 (mtmm) REVERT: G 428 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8714 (tt) REVERT: K 189 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8626 (mt) REVERT: K 295 CYS cc_start: 0.7782 (m) cc_final: 0.7519 (m) REVERT: K 304 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7661 (ttmm) REVERT: I 24 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 176 LYS cc_start: 0.8454 (mttt) cc_final: 0.8059 (mtmt) REVERT: I 346 TRP cc_start: 0.7896 (p-90) cc_final: 0.7659 (p-90) outliers start: 132 outliers final: 25 residues processed: 1906 average time/residue: 0.2573 time to fit residues: 796.0001 Evaluate side-chains 1159 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1123 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 300 ASN Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 315 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 0.4980 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 107 HIS A 228 ASN A 300 ASN A 393 HIS B 6 HIS B 28 HIS B 101 ASN B 133 GLN B 350 ASN B 385 GLN B 424 ASN B 436 GLN C 35 GLN C 101 ASN C 107 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN C 300 ASN C 393 HIS D 6 HIS D 101 ASN D 133 GLN D 136 GLN D 309 HIS D 350 ASN D 385 GLN D 436 GLN T 311 GLN T 329 GLN E 35 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS E 226 ASN E 228 ASN E 300 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN F 309 HIS F 334 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN F 436 GLN J 101 ASN J 107 HIS J 228 ASN J 300 ASN J 309 HIS J 393 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 133 GLN H 385 GLN H 424 ASN H 436 GLN L 50 ASN L 88 HIS L 101 ASN L 107 HIS L 228 ASN L 285 GLN L 300 ASN L 393 HIS G 37 HIS G 133 GLN G 136 GLN G 385 GLN G 424 ASN G 436 GLN K 35 GLN K 50 ASN K 101 ASN K 107 HIS K 226 ASN K 228 ASN K 300 ASN K 393 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN I 136 GLN I 385 GLN I 436 GLN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079115 restraints weight = 69690.796| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.13 r_work: 0.3008 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42070 Z= 0.167 Angle : 0.668 9.516 57162 Z= 0.353 Chirality : 0.045 0.176 6252 Planarity : 0.005 0.076 7436 Dihedral : 11.620 172.171 5811 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.70 % Allowed : 17.21 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 5160 helix: 2.00 (0.10), residues: 2416 sheet: 0.72 (0.18), residues: 780 loop : -0.86 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 308 TYR 0.023 0.001 TYR K 357 PHE 0.023 0.002 PHE K 255 TRP 0.019 0.003 TRP J 388 HIS 0.011 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (42070) covalent geometry : angle 0.66816 / 0.35 (57162) hydrogen bonds : bond 0.06577 / 4.45 ( 2119) hydrogen bonds : angle 5.28536 / 3.82 ( 6123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1223 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6259 (m-30) REVERT: A 155 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7140 (mp0) REVERT: A 196 GLU cc_start: 0.7330 (mp0) cc_final: 0.6762 (pm20) REVERT: A 199 ASP cc_start: 0.9011 (m-30) cc_final: 0.8476 (m-30) REVERT: A 230 LEU cc_start: 0.9191 (tt) cc_final: 0.8954 (mp) REVERT: B 110 GLU cc_start: 0.8518 (tp30) cc_final: 0.8284 (mm-30) REVERT: B 127 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8253 (mp0) REVERT: B 151 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8786 (m) REVERT: B 215 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: B 255 LEU cc_start: 0.9312 (mp) cc_final: 0.9023 (mt) REVERT: B 309 HIS cc_start: 0.8923 (m90) cc_final: 0.8089 (m-70) REVERT: B 326 LYS cc_start: 0.8877 (tttt) cc_final: 0.8519 (tptm) REVERT: B 400 ARG cc_start: 0.9193 (ttm-80) cc_final: 0.8967 (ttt90) REVERT: C 47 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.5667 (m-30) REVERT: C 112 LYS cc_start: 0.8833 (pttm) cc_final: 0.8623 (pttm) REVERT: C 199 ASP cc_start: 0.8999 (m-30) cc_final: 0.8706 (m-30) REVERT: C 213 CYS cc_start: 0.8915 (m) cc_final: 0.8535 (m) REVERT: C 230 LEU cc_start: 0.9266 (tt) cc_final: 0.9048 (mp) REVERT: C 251 ASP cc_start: 0.8252 (m-30) cc_final: 0.7868 (m-30) REVERT: C 256 GLN cc_start: 0.9151 (mt0) cc_final: 0.8874 (mt0) REVERT: C 275 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 296 PHE cc_start: 0.9068 (m-80) cc_final: 0.8841 (m-80) REVERT: C 313 MET cc_start: 0.9177 (mtm) cc_final: 0.8858 (mtt) REVERT: C 411 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7646 (mm-30) REVERT: D 90 ASP cc_start: 0.8914 (m-30) cc_final: 0.8530 (t0) REVERT: D 110 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8391 (mm-30) REVERT: D 290 GLU cc_start: 0.8829 (tp30) cc_final: 0.8607 (tt0) REVERT: D 309 HIS cc_start: 0.9193 (m90) cc_final: 0.8499 (m-70) REVERT: D 373 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8960 (mtp) REVERT: D 398 MET cc_start: 0.8859 (mtp) cc_final: 0.8515 (mtt) REVERT: D 431 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8306 (mm-30) REVERT: T 307 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7934 (p90) REVERT: E 25 CYS cc_start: 0.9252 (m) cc_final: 0.8778 (m) REVERT: E 47 ASP cc_start: 0.6794 (OUTLIER) cc_final: 0.5638 (m-30) REVERT: E 91 GLN cc_start: 0.8578 (mt0) cc_final: 0.8155 (mp10) REVERT: E 112 LYS cc_start: 0.8987 (ptpp) cc_final: 0.8450 (pttm) REVERT: E 313 MET cc_start: 0.9249 (mtm) cc_final: 0.8855 (mtm) REVERT: E 380 ASN cc_start: 0.8764 (t0) cc_final: 0.8327 (t0) REVERT: E 411 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8069 (mm-30) REVERT: E 415 GLU cc_start: 0.8672 (pm20) cc_final: 0.8063 (mt-10) REVERT: F 55 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8064 (tm-30) REVERT: F 71 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7778 (mm-30) REVERT: F 163 ASP cc_start: 0.8839 (p0) cc_final: 0.8599 (p0) REVERT: F 200 GLU cc_start: 0.9086 (pt0) cc_final: 0.8825 (pt0) REVERT: F 281 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8044 (tm-30) REVERT: F 309 HIS cc_start: 0.9143 (m90) cc_final: 0.8799 (m-70) REVERT: F 335 VAL cc_start: 0.9100 (t) cc_final: 0.8857 (m) REVERT: J 71 GLU cc_start: 0.7711 (pt0) cc_final: 0.7283 (pt0) REVERT: J 77 GLU cc_start: 0.9229 (tp30) cc_final: 0.8886 (tp30) REVERT: J 112 LYS cc_start: 0.8988 (ptpp) cc_final: 0.8784 (ptpp) REVERT: J 159 VAL cc_start: 0.9094 (t) cc_final: 0.8884 (p) REVERT: J 251 ASP cc_start: 0.8701 (m-30) cc_final: 0.8496 (m-30) REVERT: J 411 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7981 (mm-30) REVERT: J 423 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8558 (tm-30) REVERT: H 55 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7685 (tm-30) REVERT: H 76 ASP cc_start: 0.8736 (m-30) cc_final: 0.8374 (m-30) REVERT: H 110 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8252 (mt-10) REVERT: H 145 THR cc_start: 0.8629 (m) cc_final: 0.8392 (m) REVERT: H 151 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8545 (m) REVERT: H 176 LYS cc_start: 0.9096 (mttt) cc_final: 0.8850 (mppt) REVERT: H 199 ASP cc_start: 0.8338 (m-30) cc_final: 0.8137 (m-30) REVERT: H 281 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8315 (tm-30) REVERT: H 290 GLU cc_start: 0.8503 (tt0) cc_final: 0.8276 (tt0) REVERT: H 309 HIS cc_start: 0.9173 (m90) cc_final: 0.8862 (m90) REVERT: H 352 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (tttp) REVERT: H 417 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8210 (mp0) REVERT: H 420 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8696 (mm-30) REVERT: H 431 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8339 (mm-30) REVERT: L 20 CYS cc_start: 0.9169 (m) cc_final: 0.8840 (m) REVERT: L 35 GLN cc_start: 0.8522 (tt0) cc_final: 0.8226 (tp40) REVERT: L 47 ASP cc_start: 0.6449 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: L 91 GLN cc_start: 0.8611 (mt0) cc_final: 0.8288 (mt0) REVERT: L 112 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8410 (ptpp) REVERT: L 199 ASP cc_start: 0.8955 (m-30) cc_final: 0.8351 (m-30) REVERT: L 213 CYS cc_start: 0.8878 (m) cc_final: 0.8637 (m) REVERT: L 411 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7918 (mm-30) REVERT: L 433 GLU cc_start: 0.9142 (tp30) cc_final: 0.8886 (tp30) REVERT: G 24 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8808 (tt) REVERT: G 110 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8416 (mm-30) REVERT: G 149 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8641 (tpt) REVERT: G 151 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8851 (m) REVERT: G 183 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8396 (mt-10) REVERT: G 269 MET cc_start: 0.9274 (mtp) cc_final: 0.8899 (mtt) REVERT: G 293 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8352 (pp30) REVERT: G 309 HIS cc_start: 0.9233 (m90) cc_final: 0.8995 (m90) REVERT: G 431 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8629 (mm-30) REVERT: K 71 GLU cc_start: 0.8230 (pt0) cc_final: 0.7911 (tt0) REVERT: K 91 GLN cc_start: 0.8470 (mt0) cc_final: 0.8206 (mt0) REVERT: K 112 LYS cc_start: 0.8983 (pttm) cc_final: 0.8513 (pttm) REVERT: K 293 ASN cc_start: 0.9105 (m-40) cc_final: 0.8642 (m-40) REVERT: K 304 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8762 (ttmm) REVERT: K 326 LYS cc_start: 0.6287 (mmtt) cc_final: 0.5469 (ptpt) REVERT: K 411 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8153 (mm-30) REVERT: K 433 GLU cc_start: 0.9137 (tp30) cc_final: 0.8781 (tm-30) REVERT: I 12 CYS cc_start: 0.8694 (t) cc_final: 0.8337 (t) REVERT: I 24 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8592 (tt) REVERT: I 59 ASN cc_start: 0.8559 (m-40) cc_final: 0.8189 (p0) REVERT: I 202 TYR cc_start: 0.9151 (m-80) cc_final: 0.8716 (m-80) REVERT: I 211 ASP cc_start: 0.8800 (m-30) cc_final: 0.8326 (t0) REVERT: I 215 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.7836 (mtm-85) REVERT: I 281 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8443 (tm-30) REVERT: I 329 ASP cc_start: 0.8391 (m-30) cc_final: 0.7931 (m-30) REVERT: I 393 GLU cc_start: 0.9342 (tt0) cc_final: 0.9136 (tp30) REVERT: I 417 GLU cc_start: 0.8839 (mp0) cc_final: 0.8600 (mp0) outliers start: 163 outliers final: 82 residues processed: 1308 average time/residue: 0.2413 time to fit residues: 527.3987 Evaluate side-chains 1081 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 985 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 341 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 149 MET Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 219 optimal weight: 4.9990 chunk 513 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 375 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 381 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 336 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS A 226 ASN B 133 GLN C 91 GLN C 139 HIS C 226 ASN C 228 ASN D 28 HIS D 50 ASN D 293 GLN D 331 GLN D 424 ASN E 50 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 133 GLN F 331 GLN F 334 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN J 139 HIS J 226 ASN J 300 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 HIS ** J 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 37 HIS ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 226 ASN L 342 GLN K 88 HIS K 139 HIS K 380 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 329 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076407 restraints weight = 72498.032| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.13 r_work: 0.2944 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 42070 Z= 0.185 Angle : 0.606 9.832 57162 Z= 0.320 Chirality : 0.043 0.157 6252 Planarity : 0.004 0.045 7436 Dihedral : 10.978 172.824 5789 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.44 % Allowed : 17.30 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.12), residues: 5160 helix: 2.01 (0.10), residues: 2440 sheet: 0.68 (0.19), residues: 762 loop : -0.70 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 121 TYR 0.021 0.001 TYR G 161 PHE 0.031 0.002 PHE E 255 TRP 0.017 0.002 TRP I 346 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (42070) covalent geometry : angle 0.60647 / 0.32 (57162) hydrogen bonds : bond 0.05611 / 3.78 ( 2119) hydrogen bonds : angle 4.87705 / 3.53 ( 6123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1055 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6237 (m-30) REVERT: A 123 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8601 (tpp80) REVERT: A 196 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6735 (pm20) REVERT: A 199 ASP cc_start: 0.8979 (m-30) cc_final: 0.8386 (m-30) REVERT: A 269 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 308 ARG cc_start: 0.9290 (mtm-85) cc_final: 0.8979 (mtm-85) REVERT: A 349 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8624 (t) REVERT: A 411 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 415 GLU cc_start: 0.8558 (pm20) cc_final: 0.8117 (mt-10) REVERT: B 59 ASN cc_start: 0.8325 (m110) cc_final: 0.8046 (p0) REVERT: B 127 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8337 (mp0) REVERT: B 151 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8906 (m) REVERT: B 215 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7417 (mtt90) REVERT: B 259 MET cc_start: 0.8761 (mmp) cc_final: 0.8116 (mmp) REVERT: B 284 ARG cc_start: 0.8383 (ptm160) cc_final: 0.8151 (ptm160) REVERT: B 309 HIS cc_start: 0.8959 (m90) cc_final: 0.8000 (m-70) REVERT: B 326 LYS cc_start: 0.9038 (tttt) cc_final: 0.8747 (tptm) REVERT: B 349 ASN cc_start: 0.7907 (t0) cc_final: 0.7462 (t0) REVERT: B 400 ARG cc_start: 0.9208 (ttm-80) cc_final: 0.8929 (ttt90) REVERT: C 47 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.5962 (m-30) REVERT: C 196 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: C 199 ASP cc_start: 0.8997 (m-30) cc_final: 0.8713 (m-30) REVERT: C 213 CYS cc_start: 0.8876 (m) cc_final: 0.8518 (m) REVERT: C 230 LEU cc_start: 0.9347 (tt) cc_final: 0.9056 (mp) REVERT: C 251 ASP cc_start: 0.8431 (m-30) cc_final: 0.8138 (m-30) REVERT: C 254 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 256 GLN cc_start: 0.9211 (mt0) cc_final: 0.8877 (mt0) REVERT: C 285 GLN cc_start: 0.3507 (mm-40) cc_final: 0.3115 (mm110) REVERT: C 411 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 423 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8619 (mp0) REVERT: C 433 GLU cc_start: 0.9106 (tp30) cc_final: 0.8867 (tm-30) REVERT: D 50 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8794 (p0) REVERT: D 53 TYR cc_start: 0.9038 (m-80) cc_final: 0.8580 (m-80) REVERT: D 55 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7957 (tm-30) REVERT: D 71 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8006 (tt0) REVERT: D 110 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 209 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8868 (mp) REVERT: D 278 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8372 (tpm170) REVERT: D 281 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 309 HIS cc_start: 0.9230 (m90) cc_final: 0.8589 (m-70) REVERT: D 398 MET cc_start: 0.8886 (mtp) cc_final: 0.8643 (mtt) REVERT: D 416 MET cc_start: 0.8791 (mmm) cc_final: 0.8582 (mmm) REVERT: D 431 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8175 (mm-30) REVERT: E 47 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.5914 (m-30) REVERT: E 76 ASP cc_start: 0.8902 (m-30) cc_final: 0.8670 (m-30) REVERT: E 77 GLU cc_start: 0.9358 (tp30) cc_final: 0.8992 (tp30) REVERT: E 91 GLN cc_start: 0.8751 (mt0) cc_final: 0.8513 (mt0) REVERT: E 313 MET cc_start: 0.9246 (mtm) cc_final: 0.8270 (mtm) REVERT: E 380 ASN cc_start: 0.8744 (t0) cc_final: 0.8020 (t0) REVERT: E 411 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8079 (mm-30) REVERT: E 415 GLU cc_start: 0.8697 (pm20) cc_final: 0.8148 (mt-10) REVERT: E 417 GLU cc_start: 0.8221 (mp0) cc_final: 0.7949 (mp0) REVERT: E 430 LYS cc_start: 0.9116 (tppp) cc_final: 0.8518 (tppt) REVERT: E 433 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8881 (tm-30) REVERT: F 71 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7807 (mm-30) REVERT: F 196 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: F 281 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 339 ASN cc_start: 0.8182 (m-40) cc_final: 0.7970 (m-40) REVERT: F 349 ASN cc_start: 0.8027 (t0) cc_final: 0.7720 (t0) REVERT: F 386 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8572 (pt0) REVERT: F 415 GLU cc_start: 0.8723 (pm20) cc_final: 0.8430 (pm20) REVERT: F 431 GLU cc_start: 0.8993 (tt0) cc_final: 0.8580 (mt-10) REVERT: J 24 TYR cc_start: 0.8776 (m-80) cc_final: 0.8305 (m-80) REVERT: J 71 GLU cc_start: 0.7805 (pt0) cc_final: 0.7261 (pt0) REVERT: J 313 MET cc_start: 0.9393 (mtt) cc_final: 0.8639 (mtm) REVERT: J 380 ASN cc_start: 0.8876 (t0) cc_final: 0.7935 (t0) REVERT: J 411 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7819 (mm-30) REVERT: J 413 MET cc_start: 0.8189 (tpp) cc_final: 0.7445 (tpp) REVERT: J 420 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8375 (mm-30) REVERT: J 423 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8682 (tm-30) REVERT: H 37 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8397 (m90) REVERT: H 55 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7683 (tm-30) REVERT: H 76 ASP cc_start: 0.8731 (m-30) cc_final: 0.8296 (m-30) REVERT: H 110 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8230 (mt-10) REVERT: H 145 THR cc_start: 0.8540 (m) cc_final: 0.8326 (m) REVERT: H 176 LYS cc_start: 0.9090 (mttt) cc_final: 0.8801 (mppt) REVERT: H 199 ASP cc_start: 0.8340 (m-30) cc_final: 0.8022 (m-30) REVERT: H 205 ASP cc_start: 0.8721 (t0) cc_final: 0.7495 (t70) REVERT: H 209 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8724 (mp) REVERT: H 281 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8327 (tm-30) REVERT: H 322 ARG cc_start: 0.9058 (mtt-85) cc_final: 0.8840 (mmm-85) REVERT: H 352 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8530 (tttp) REVERT: H 428 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8942 (tt) REVERT: H 431 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8344 (mm-30) REVERT: L 20 CYS cc_start: 0.9184 (m) cc_final: 0.8881 (m) REVERT: L 35 GLN cc_start: 0.8676 (tt0) cc_final: 0.8391 (tp40) REVERT: L 47 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.5805 (m-30) REVERT: L 91 GLN cc_start: 0.8609 (mt0) cc_final: 0.8133 (mt0) REVERT: L 113 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8262 (mp0) REVERT: L 199 ASP cc_start: 0.8974 (m-30) cc_final: 0.8387 (m-30) REVERT: L 213 CYS cc_start: 0.8869 (m) cc_final: 0.8592 (m) REVERT: L 411 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8006 (mm-30) REVERT: L 423 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8241 (mt-10) REVERT: L 425 MET cc_start: 0.9177 (tpt) cc_final: 0.8921 (tpt) REVERT: L 433 GLU cc_start: 0.9116 (tp30) cc_final: 0.8826 (tp30) REVERT: G 151 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8802 (m) REVERT: G 160 GLU cc_start: 0.8869 (tp30) cc_final: 0.8618 (tp30) REVERT: G 269 MET cc_start: 0.9270 (mtp) cc_final: 0.8961 (mtt) REVERT: G 293 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8434 (pp30) REVERT: G 309 HIS cc_start: 0.9342 (m90) cc_final: 0.9139 (m90) REVERT: K 71 GLU cc_start: 0.8220 (pt0) cc_final: 0.7881 (tt0) REVERT: K 91 GLN cc_start: 0.8635 (mt0) cc_final: 0.8336 (mt0) REVERT: K 112 LYS cc_start: 0.9059 (pttm) cc_final: 0.8451 (pttm) REVERT: K 293 ASN cc_start: 0.9151 (m-40) cc_final: 0.8647 (m110) REVERT: K 304 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8849 (ttmm) REVERT: K 326 LYS cc_start: 0.6132 (mmtt) cc_final: 0.5364 (ptpt) REVERT: K 411 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8015 (mm-30) REVERT: K 415 GLU cc_start: 0.8006 (pm20) cc_final: 0.7788 (pm20) REVERT: I 12 CYS cc_start: 0.8726 (t) cc_final: 0.8291 (t) REVERT: I 24 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8802 (tt) REVERT: I 47 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8137 (mm-30) REVERT: I 59 ASN cc_start: 0.8656 (m-40) cc_final: 0.8273 (p0) REVERT: I 71 GLU cc_start: 0.8439 (tp30) cc_final: 0.8056 (tm-30) REVERT: I 211 ASP cc_start: 0.8809 (m-30) cc_final: 0.8346 (t0) REVERT: I 215 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.7857 (mtm-85) REVERT: I 309 HIS cc_start: 0.9345 (m90) cc_final: 0.8928 (m90) REVERT: I 329 ASP cc_start: 0.8214 (m-30) cc_final: 0.7941 (m-30) REVERT: I 346 TRP cc_start: 0.9176 (p-90) cc_final: 0.8565 (p-90) REVERT: I 386 GLU cc_start: 0.8787 (pt0) cc_final: 0.8536 (pt0) REVERT: I 393 GLU cc_start: 0.9338 (tt0) cc_final: 0.8996 (tp30) outliers start: 196 outliers final: 120 residues processed: 1163 average time/residue: 0.2296 time to fit residues: 450.2262 Evaluate side-chains 1083 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 945 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 357 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 191 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 411 optimal weight: 3.9990 chunk 493 optimal weight: 5.9990 chunk 417 optimal weight: 0.8980 chunk 419 optimal weight: 9.9990 chunk 481 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 494 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN T 311 GLN E 258 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 50 ASN H 136 GLN H 349 ASN L 139 HIS L 192 HIS ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071855 restraints weight = 74019.704| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.15 r_work: 0.2876 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 42070 Z= 0.275 Angle : 0.645 10.376 57162 Z= 0.340 Chirality : 0.045 0.160 6252 Planarity : 0.005 0.061 7436 Dihedral : 10.725 174.012 5781 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.63 % Allowed : 18.16 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 5160 helix: 1.76 (0.10), residues: 2446 sheet: 1.11 (0.20), residues: 714 loop : -0.70 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 121 TYR 0.017 0.002 TYR I 283 PHE 0.029 0.002 PHE E 255 TRP 0.017 0.002 TRP I 346 HIS 0.028 0.002 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 (42070) covalent geometry : angle 0.64464 / 0.34 (57162) hydrogen bonds : bond 0.06182 / 4.18 ( 2119) hydrogen bonds : angle 4.88043 / 3.53 ( 6123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 934 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: A 123 ARG cc_start: 0.9091 (tpp80) cc_final: 0.8752 (tpp80) REVERT: A 196 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 254 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 285 GLN cc_start: 0.8126 (tt0) cc_final: 0.7755 (pt0) REVERT: A 349 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8688 (t) REVERT: A 411 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 430 LYS cc_start: 0.8961 (tppp) cc_final: 0.8612 (tppp) REVERT: B 110 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8259 (mp0) REVERT: B 151 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8868 (m) REVERT: B 179 ASP cc_start: 0.8922 (t0) cc_final: 0.8423 (t0) REVERT: B 215 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7639 (mtt90) REVERT: B 259 MET cc_start: 0.8851 (mmp) cc_final: 0.8234 (mmp) REVERT: B 281 GLN cc_start: 0.8705 (tp40) cc_final: 0.8232 (tp40) REVERT: B 299 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8404 (mmtm) REVERT: B 309 HIS cc_start: 0.8953 (m90) cc_final: 0.8243 (m-70) REVERT: B 326 LYS cc_start: 0.9179 (tttt) cc_final: 0.8911 (tptm) REVERT: B 349 ASN cc_start: 0.8022 (t0) cc_final: 0.7648 (t0) REVERT: B 400 ARG cc_start: 0.9238 (ttm-80) cc_final: 0.8953 (ttt90) REVERT: C 47 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6708 (m-30) REVERT: C 127 ASP cc_start: 0.8620 (m-30) cc_final: 0.8364 (m-30) REVERT: C 196 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: C 199 ASP cc_start: 0.9042 (m-30) cc_final: 0.8783 (m-30) REVERT: C 251 ASP cc_start: 0.8450 (m-30) cc_final: 0.8151 (m-30) REVERT: C 285 GLN cc_start: 0.3456 (mm-40) cc_final: 0.2983 (mm110) REVERT: C 313 MET cc_start: 0.9149 (mtm) cc_final: 0.8580 (mtm) REVERT: C 315 CYS cc_start: 0.8874 (m) cc_final: 0.8639 (m) REVERT: C 396 ASP cc_start: 0.9376 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: C 411 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 423 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8596 (mp0) REVERT: C 430 LYS cc_start: 0.9275 (mmmm) cc_final: 0.9035 (tppt) REVERT: D 71 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7889 (mm-30) REVERT: D 90 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8550 (t0) REVERT: D 109 THR cc_start: 0.9137 (m) cc_final: 0.8141 (p) REVERT: D 113 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8309 (mm-30) REVERT: D 166 MET cc_start: 0.9285 (tpp) cc_final: 0.9024 (tpt) REVERT: D 209 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8999 (mp) REVERT: D 278 ARG cc_start: 0.8768 (mmm160) cc_final: 0.8343 (tpm170) REVERT: D 281 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8363 (tm-30) REVERT: D 290 GLU cc_start: 0.8487 (tt0) cc_final: 0.8260 (tt0) REVERT: D 293 GLN cc_start: 0.9009 (pt0) cc_final: 0.8786 (pp30) REVERT: D 309 HIS cc_start: 0.9214 (m90) cc_final: 0.8508 (m-70) REVERT: D 398 MET cc_start: 0.9100 (mtp) cc_final: 0.8824 (mtt) REVERT: D 417 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8355 (mt-10) REVERT: D 431 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8009 (mm-30) REVERT: E 47 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6018 (m-30) REVERT: E 76 ASP cc_start: 0.8868 (m-30) cc_final: 0.8582 (m-30) REVERT: E 77 GLU cc_start: 0.9392 (tp30) cc_final: 0.9024 (tp30) REVERT: E 91 GLN cc_start: 0.8871 (mt0) cc_final: 0.8464 (mt0) REVERT: E 254 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7813 (mt-10) REVERT: E 285 GLN cc_start: 0.8402 (tt0) cc_final: 0.7911 (pt0) REVERT: E 313 MET cc_start: 0.9291 (mtm) cc_final: 0.8238 (mtm) REVERT: E 380 ASN cc_start: 0.8958 (t0) cc_final: 0.7970 (t0) REVERT: E 411 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8171 (mm-30) REVERT: E 424 ASP cc_start: 0.9179 (m-30) cc_final: 0.8851 (m-30) REVERT: E 430 LYS cc_start: 0.9226 (tppp) cc_final: 0.8749 (tppt) REVERT: F 71 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7807 (mm-30) REVERT: F 281 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 349 ASN cc_start: 0.8287 (t0) cc_final: 0.7974 (t0) REVERT: F 386 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8399 (pt0) REVERT: F 415 GLU cc_start: 0.8687 (pm20) cc_final: 0.8075 (pm20) REVERT: F 416 MET cc_start: 0.8817 (mmm) cc_final: 0.8345 (mmm) REVERT: J 69 ASP cc_start: 0.8439 (t0) cc_final: 0.8142 (t0) REVERT: J 71 GLU cc_start: 0.7936 (pt0) cc_final: 0.7411 (pt0) REVERT: J 76 ASP cc_start: 0.8905 (m-30) cc_final: 0.8394 (m-30) REVERT: J 112 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8677 (ptpp) REVERT: J 230 LEU cc_start: 0.9329 (tp) cc_final: 0.8975 (mp) REVERT: J 411 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8017 (mm-30) REVERT: J 420 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8414 (mm-30) REVERT: J 423 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8673 (tm-30) REVERT: H 55 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7642 (tm-30) REVERT: H 71 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8412 (tp30) REVERT: H 76 ASP cc_start: 0.8825 (m-30) cc_final: 0.8349 (m-30) REVERT: H 110 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8263 (mt-10) REVERT: H 199 ASP cc_start: 0.8415 (m-30) cc_final: 0.8065 (m-30) REVERT: H 205 ASP cc_start: 0.8828 (t0) cc_final: 0.7667 (t70) REVERT: H 281 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 322 ARG cc_start: 0.9161 (mtt-85) cc_final: 0.8927 (mmm-85) REVERT: H 352 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (tttp) REVERT: H 428 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9084 (tt) REVERT: H 431 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8353 (mm-30) REVERT: L 47 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: L 76 ASP cc_start: 0.8925 (m-30) cc_final: 0.8660 (m-30) REVERT: L 91 GLN cc_start: 0.8281 (mt0) cc_final: 0.7516 (mt0) REVERT: L 112 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8498 (ptpp) REVERT: L 113 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8236 (mp0) REVERT: L 199 ASP cc_start: 0.8945 (m-30) cc_final: 0.8407 (m-30) REVERT: L 213 CYS cc_start: 0.8837 (m) cc_final: 0.8569 (m) REVERT: L 411 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8108 (mm-30) REVERT: L 415 GLU cc_start: 0.8404 (pm20) cc_final: 0.8181 (pm20) REVERT: L 423 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8130 (mt-10) REVERT: L 425 MET cc_start: 0.9216 (tpt) cc_final: 0.8943 (tpt) REVERT: L 433 GLU cc_start: 0.9246 (tp30) cc_final: 0.8959 (tp30) REVERT: G 1 MET cc_start: 0.9027 (mmm) cc_final: 0.8675 (mmm) REVERT: G 24 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8881 (tt) REVERT: G 151 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8749 (m) REVERT: G 160 GLU cc_start: 0.8963 (tp30) cc_final: 0.8622 (tp30) REVERT: G 242 LEU cc_start: 0.9016 (mt) cc_final: 0.8771 (mp) REVERT: G 293 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8596 (pp30) REVERT: G 386 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8640 (pp20) REVERT: K 76 ASP cc_start: 0.8875 (m-30) cc_final: 0.8445 (m-30) REVERT: K 112 LYS cc_start: 0.9025 (pttm) cc_final: 0.8382 (pttm) REVERT: K 293 ASN cc_start: 0.9143 (m-40) cc_final: 0.8617 (m110) REVERT: K 326 LYS cc_start: 0.6250 (mmtt) cc_final: 0.5184 (ptpt) REVERT: K 357 TYR cc_start: 0.8848 (m-80) cc_final: 0.8567 (m-80) REVERT: K 390 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8483 (mtm180) REVERT: K 396 ASP cc_start: 0.8725 (m-30) cc_final: 0.8208 (m-30) REVERT: K 411 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8253 (mm-30) REVERT: I 12 CYS cc_start: 0.8855 (t) cc_final: 0.8391 (t) REVERT: I 47 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8064 (mm-30) REVERT: I 59 ASN cc_start: 0.8601 (m-40) cc_final: 0.8206 (p0) REVERT: I 71 GLU cc_start: 0.8506 (tp30) cc_final: 0.8142 (tm-30) REVERT: I 127 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8530 (mm-30) REVERT: I 205 ASP cc_start: 0.8587 (t0) cc_final: 0.8318 (t0) REVERT: I 211 ASP cc_start: 0.8900 (m-30) cc_final: 0.8328 (t0) REVERT: I 215 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.7723 (mtm-85) REVERT: I 309 HIS cc_start: 0.9387 (m90) cc_final: 0.9106 (m-70) REVERT: I 329 ASP cc_start: 0.8288 (m-30) cc_final: 0.8073 (m-30) REVERT: I 386 GLU cc_start: 0.8802 (pt0) cc_final: 0.8403 (pt0) REVERT: I 405 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9072 (tt) outliers start: 204 outliers final: 136 residues processed: 1054 average time/residue: 0.2359 time to fit residues: 415.0054 Evaluate side-chains 1035 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 882 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 295 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 225 THR Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 384 ILE Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain I residue 428 LEU Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 451 optimal weight: 0.0170 chunk 190 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 440 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 59 ASN T 311 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 309 HIS H 349 ASN L 31 GLN L 342 GLN G 258 ASN G 336 GLN G 349 ASN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 136 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075333 restraints weight = 72042.958| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.09 r_work: 0.2944 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 42070 Z= 0.136 Angle : 0.565 9.315 57162 Z= 0.295 Chirality : 0.043 0.149 6252 Planarity : 0.004 0.055 7436 Dihedral : 10.423 174.013 5774 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.51 % Allowed : 19.32 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5160 helix: 1.88 (0.10), residues: 2440 sheet: 1.27 (0.20), residues: 714 loop : -0.64 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 278 TYR 0.017 0.001 TYR L 185 PHE 0.026 0.001 PHE E 255 TRP 0.019 0.002 TRP I 346 HIS 0.014 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (42070) covalent geometry : angle 0.56476 / 0.30 (57162) hydrogen bonds : bond 0.04948 / 3.34 ( 2119) hydrogen bonds : angle 4.60213 / 3.32 ( 6123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1011 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6232 (m-30) REVERT: A 123 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8791 (tpp80) REVERT: A 196 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: A 254 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 415 GLU cc_start: 0.8661 (pm20) cc_final: 0.8171 (mt-10) REVERT: A 430 LYS cc_start: 0.9010 (tppp) cc_final: 0.8615 (tppp) REVERT: B 110 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8211 (mp0) REVERT: B 124 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8687 (tttp) REVERT: B 179 ASP cc_start: 0.8858 (t0) cc_final: 0.8245 (t0) REVERT: B 215 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7712 (mtt90) REVERT: B 259 MET cc_start: 0.8827 (mmp) cc_final: 0.8376 (mmp) REVERT: B 281 GLN cc_start: 0.8741 (tp40) cc_final: 0.8247 (tp40) REVERT: B 309 HIS cc_start: 0.9051 (m90) cc_final: 0.8387 (m-70) REVERT: B 349 ASN cc_start: 0.7980 (t0) cc_final: 0.7609 (t0) REVERT: B 400 ARG cc_start: 0.9161 (ttm-80) cc_final: 0.8938 (ttt90) REVERT: C 47 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6839 (m-30) REVERT: C 90 GLU cc_start: 0.8797 (tt0) cc_final: 0.8435 (tt0) REVERT: C 127 ASP cc_start: 0.8592 (m-30) cc_final: 0.8360 (m-30) REVERT: C 196 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: C 199 ASP cc_start: 0.8985 (m-30) cc_final: 0.8715 (m-30) REVERT: C 251 ASP cc_start: 0.8555 (m-30) cc_final: 0.8225 (m-30) REVERT: C 254 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8192 (mt-10) REVERT: C 285 GLN cc_start: 0.3651 (mm-40) cc_final: 0.3254 (mm110) REVERT: C 290 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8466 (mt-10) REVERT: C 309 HIS cc_start: 0.8573 (m90) cc_final: 0.8328 (m90) REVERT: C 313 MET cc_start: 0.9099 (mtm) cc_final: 0.8234 (mtm) REVERT: C 315 CYS cc_start: 0.8751 (m) cc_final: 0.8452 (m) REVERT: C 377 MET cc_start: 0.9015 (ttp) cc_final: 0.8376 (tmm) REVERT: C 392 ASP cc_start: 0.8755 (m-30) cc_final: 0.8475 (t0) REVERT: C 396 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9005 (m-30) REVERT: C 411 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7800 (mm-30) REVERT: C 423 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8822 (mp0) REVERT: C 430 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9054 (tppt) REVERT: C 433 GLU cc_start: 0.9188 (tp30) cc_final: 0.8867 (tm-30) REVERT: D 50 ASN cc_start: 0.9114 (p0) cc_final: 0.8804 (p0) REVERT: D 53 TYR cc_start: 0.8959 (m-80) cc_final: 0.8653 (m-80) REVERT: D 71 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7931 (mm-30) REVERT: D 109 THR cc_start: 0.9088 (m) cc_final: 0.8277 (p) REVERT: D 113 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8298 (mm-30) REVERT: D 127 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8510 (mp0) REVERT: D 166 MET cc_start: 0.9155 (tpp) cc_final: 0.8906 (tpt) REVERT: D 209 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8939 (mp) REVERT: D 240 THR cc_start: 0.8626 (m) cc_final: 0.8278 (m) REVERT: D 259 MET cc_start: 0.8610 (mmp) cc_final: 0.7849 (mmt) REVERT: D 278 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8265 (tpm170) REVERT: D 281 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8284 (tm-30) REVERT: D 293 GLN cc_start: 0.8940 (pt0) cc_final: 0.8712 (pp30) REVERT: D 309 HIS cc_start: 0.9228 (m90) cc_final: 0.8413 (m90) REVERT: D 398 MET cc_start: 0.8955 (mtp) cc_final: 0.8723 (mtt) REVERT: D 431 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7932 (mm-30) REVERT: E 47 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.5496 (m-30) REVERT: E 91 GLN cc_start: 0.8821 (mt0) cc_final: 0.8524 (mt0) REVERT: E 254 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 285 GLN cc_start: 0.8434 (tt0) cc_final: 0.7971 (pt0) REVERT: E 313 MET cc_start: 0.9317 (mtm) cc_final: 0.8188 (mtm) REVERT: E 380 ASN cc_start: 0.8951 (t0) cc_final: 0.7954 (t0) REVERT: E 396 ASP cc_start: 0.9239 (t70) cc_final: 0.8998 (m-30) REVERT: E 411 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 415 GLU cc_start: 0.8563 (pm20) cc_final: 0.7970 (mt-10) REVERT: E 420 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8717 (mm-30) REVERT: E 424 ASP cc_start: 0.9123 (m-30) cc_final: 0.8798 (m-30) REVERT: E 430 LYS cc_start: 0.9151 (tppp) cc_final: 0.8597 (tppt) REVERT: E 433 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8870 (tm-30) REVERT: F 71 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7826 (mm-30) REVERT: F 163 ASP cc_start: 0.9058 (p0) cc_final: 0.8830 (p0) REVERT: F 196 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: F 278 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7229 (tpm170) REVERT: F 281 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8196 (tm-30) REVERT: F 309 HIS cc_start: 0.8991 (m90) cc_final: 0.8698 (m90) REVERT: F 326 LYS cc_start: 0.9140 (tttt) cc_final: 0.8899 (tptp) REVERT: F 349 ASN cc_start: 0.8267 (t0) cc_final: 0.7900 (t0) REVERT: F 386 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8471 (pt0) REVERT: F 411 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8726 (mm-30) REVERT: F 415 GLU cc_start: 0.8611 (pm20) cc_final: 0.8238 (pm20) REVERT: F 416 MET cc_start: 0.8792 (mmm) cc_final: 0.8255 (mmm) REVERT: F 431 GLU cc_start: 0.8879 (tt0) cc_final: 0.8532 (mt-10) REVERT: J 69 ASP cc_start: 0.8347 (t0) cc_final: 0.8122 (t0) REVERT: J 71 GLU cc_start: 0.7930 (pt0) cc_final: 0.7274 (pt0) REVERT: J 76 ASP cc_start: 0.8884 (m-30) cc_final: 0.8517 (m-30) REVERT: J 112 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8728 (pttm) REVERT: J 150 THR cc_start: 0.9179 (m) cc_final: 0.8953 (m) REVERT: J 230 LEU cc_start: 0.9302 (tp) cc_final: 0.9047 (mp) REVERT: J 357 TYR cc_start: 0.9007 (m-80) cc_final: 0.8790 (m-80) REVERT: J 380 ASN cc_start: 0.8894 (t0) cc_final: 0.8658 (t0) REVERT: J 411 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7955 (mm-30) REVERT: J 420 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8662 (mm-30) REVERT: J 423 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8467 (tm-30) REVERT: H 55 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7603 (tm-30) REVERT: H 71 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8114 (tp30) REVERT: H 76 ASP cc_start: 0.8847 (m-30) cc_final: 0.8347 (m-30) REVERT: H 110 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8403 (mt-10) REVERT: H 160 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8398 (tp30) REVERT: H 179 ASP cc_start: 0.6769 (t0) cc_final: 0.6315 (t0) REVERT: H 205 ASP cc_start: 0.8754 (t0) cc_final: 0.7511 (t70) REVERT: H 281 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8269 (tm-30) REVERT: H 332 MET cc_start: 0.9302 (mmt) cc_final: 0.9095 (mmt) REVERT: H 352 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8630 (tttp) REVERT: H 431 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8335 (mm-30) REVERT: H 435 TYR cc_start: 0.8787 (m-80) cc_final: 0.8476 (m-80) REVERT: L 20 CYS cc_start: 0.9089 (m) cc_final: 0.8669 (m) REVERT: L 24 TYR cc_start: 0.8938 (m-80) cc_final: 0.8582 (m-80) REVERT: L 47 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6115 (m-30) REVERT: L 76 ASP cc_start: 0.8957 (m-30) cc_final: 0.8658 (m-30) REVERT: L 91 GLN cc_start: 0.8155 (mt0) cc_final: 0.7794 (mt0) REVERT: L 112 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8623 (ptpp) REVERT: L 113 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8210 (mp0) REVERT: L 120 ASP cc_start: 0.9096 (t0) cc_final: 0.8876 (t0) REVERT: L 196 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8562 (mp0) REVERT: L 199 ASP cc_start: 0.8908 (m-30) cc_final: 0.8399 (m-30) REVERT: L 411 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8075 (mm-30) REVERT: L 425 MET cc_start: 0.9247 (tpt) cc_final: 0.9038 (tpt) REVERT: L 430 LYS cc_start: 0.9236 (tppt) cc_final: 0.8997 (tppt) REVERT: L 433 GLU cc_start: 0.9206 (tp30) cc_final: 0.8810 (tp30) REVERT: G 151 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8813 (m) REVERT: G 160 GLU cc_start: 0.8963 (tp30) cc_final: 0.8600 (tp30) REVERT: G 199 ASP cc_start: 0.7899 (m-30) cc_final: 0.7691 (m-30) REVERT: G 293 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8558 (pp30) REVERT: G 386 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: K 112 LYS cc_start: 0.9051 (pttm) cc_final: 0.8573 (pttm) REVERT: K 168 GLU cc_start: 0.8679 (pt0) cc_final: 0.8440 (pt0) REVERT: K 254 GLU cc_start: 0.4088 (mm-30) cc_final: 0.3705 (mm-30) REVERT: K 293 ASN cc_start: 0.9118 (m-40) cc_final: 0.8606 (m110) REVERT: K 326 LYS cc_start: 0.6106 (mmtt) cc_final: 0.5210 (ptpt) REVERT: K 390 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8425 (mtm180) REVERT: K 411 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8214 (mm-30) REVERT: K 415 GLU cc_start: 0.8145 (pm20) cc_final: 0.7532 (mt-10) REVERT: I 12 CYS cc_start: 0.8594 (t) cc_final: 0.8177 (t) REVERT: I 47 GLU cc_start: 0.8646 (mm-30) cc_final: 0.7965 (mm-30) REVERT: I 59 ASN cc_start: 0.8665 (m-40) cc_final: 0.8276 (p0) REVERT: I 71 GLU cc_start: 0.8477 (tp30) cc_final: 0.8149 (tm-30) REVERT: I 176 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8958 (mppt) REVERT: I 205 ASP cc_start: 0.8502 (t0) cc_final: 0.8263 (t0) REVERT: I 211 ASP cc_start: 0.8862 (m-30) cc_final: 0.8360 (t0) REVERT: I 215 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7750 (mtm-85) REVERT: I 278 ARG cc_start: 0.8262 (tpm170) cc_final: 0.7957 (tpm170) REVERT: I 309 HIS cc_start: 0.9376 (m90) cc_final: 0.9089 (m-70) REVERT: I 329 ASP cc_start: 0.8213 (m-30) cc_final: 0.7973 (m-30) REVERT: I 386 GLU cc_start: 0.8721 (pt0) cc_final: 0.8334 (pt0) outliers start: 155 outliers final: 96 residues processed: 1101 average time/residue: 0.2411 time to fit residues: 442.7774 Evaluate side-chains 1054 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 945 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 278 ARG Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 386 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain P residue 307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 481 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 470 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 322 optimal weight: 0.0770 chunk 16 optimal weight: 0.3980 chunk 437 optimal weight: 4.9990 chunk 482 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN D 59 ASN T 311 GLN E 197 HIS E 256 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 349 ASN G 349 ASN K 192 HIS K 256 GLN K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 330 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076943 restraints weight = 72121.627| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.18 r_work: 0.2971 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 42070 Z= 0.117 Angle : 0.557 9.673 57162 Z= 0.288 Chirality : 0.042 0.239 6252 Planarity : 0.004 0.051 7436 Dihedral : 10.129 171.398 5774 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.17 % Allowed : 19.93 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5160 helix: 1.84 (0.10), residues: 2464 sheet: 1.13 (0.19), residues: 756 loop : -0.59 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 400 TYR 0.014 0.001 TYR L 319 PHE 0.022 0.001 PHE E 255 TRP 0.023 0.002 TRP I 346 HIS 0.043 0.001 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (42070) covalent geometry : angle 0.55691 / 0.29 (57162) hydrogen bonds : bond 0.04370 / 2.95 ( 2119) hydrogen bonds : angle 4.48638 / 3.24 ( 6123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1036 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6192 (m-30) REVERT: A 123 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8746 (tpp80) REVERT: A 156 ARG cc_start: 0.9070 (mmt90) cc_final: 0.8495 (mmm-85) REVERT: A 176 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8661 (mm110) REVERT: A 196 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: A 338 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8319 (ttmm) REVERT: A 415 GLU cc_start: 0.8667 (pm20) cc_final: 0.8112 (mt-10) REVERT: A 430 LYS cc_start: 0.8996 (tppp) cc_final: 0.8606 (tppp) REVERT: B 124 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8694 (tttp) REVERT: B 193 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8331 (mp10) REVERT: B 215 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7592 (mtt90) REVERT: B 259 MET cc_start: 0.8644 (mmp) cc_final: 0.8268 (mmp) REVERT: B 281 GLN cc_start: 0.8795 (tp40) cc_final: 0.8229 (tp40) REVERT: B 284 ARG cc_start: 0.8237 (ptm160) cc_final: 0.8032 (ptm160) REVERT: B 309 HIS cc_start: 0.9042 (m90) cc_final: 0.8381 (m-70) REVERT: B 349 ASN cc_start: 0.8058 (t0) cc_final: 0.7855 (t0) REVERT: B 400 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8972 (ttt90) REVERT: B 415 GLU cc_start: 0.8611 (pm20) cc_final: 0.7995 (pm20) REVERT: B 416 MET cc_start: 0.8833 (mmm) cc_final: 0.7988 (mmm) REVERT: C 47 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6195 (m-30) REVERT: C 69 ASP cc_start: 0.8461 (t0) cc_final: 0.7796 (t0) REVERT: C 90 GLU cc_start: 0.8680 (tt0) cc_final: 0.8379 (tt0) REVERT: C 127 ASP cc_start: 0.8551 (m-30) cc_final: 0.8316 (m-30) REVERT: C 196 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: C 199 ASP cc_start: 0.8922 (m-30) cc_final: 0.8700 (m-30) REVERT: C 285 GLN cc_start: 0.3749 (mm-40) cc_final: 0.3323 (mm110) REVERT: C 377 MET cc_start: 0.9043 (ttp) cc_final: 0.8831 (tmm) REVERT: C 392 ASP cc_start: 0.8780 (m-30) cc_final: 0.8488 (t0) REVERT: C 396 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9038 (m-30) REVERT: C 420 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8688 (mm-30) REVERT: C 423 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9054 (pp20) REVERT: D 50 ASN cc_start: 0.9173 (p0) cc_final: 0.8847 (p0) REVERT: D 53 TYR cc_start: 0.8924 (m-80) cc_final: 0.8509 (m-80) REVERT: D 71 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8078 (tt0) REVERT: D 166 MET cc_start: 0.9172 (tpp) cc_final: 0.8903 (tpt) REVERT: D 176 LYS cc_start: 0.9348 (mtpp) cc_final: 0.9130 (mtpp) REVERT: D 209 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8881 (mp) REVERT: D 240 THR cc_start: 0.8541 (m) cc_final: 0.8189 (m) REVERT: D 259 MET cc_start: 0.8524 (mmp) cc_final: 0.7731 (mmt) REVERT: D 278 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8375 (tpm170) REVERT: D 281 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8401 (tm-30) REVERT: D 290 GLU cc_start: 0.8646 (tt0) cc_final: 0.8261 (tt0) REVERT: D 293 GLN cc_start: 0.8952 (pt0) cc_final: 0.8694 (pp30) REVERT: D 309 HIS cc_start: 0.9201 (m90) cc_final: 0.8269 (m90) REVERT: D 431 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: E 47 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.5447 (t0) REVERT: E 91 GLN cc_start: 0.8771 (mt0) cc_final: 0.8389 (mp10) REVERT: E 254 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7769 (mt-10) REVERT: E 285 GLN cc_start: 0.8217 (tt0) cc_final: 0.7958 (pt0) REVERT: E 313 MET cc_start: 0.9378 (mtm) cc_final: 0.8520 (mtm) REVERT: E 380 ASN cc_start: 0.8986 (t0) cc_final: 0.7883 (t0) REVERT: E 396 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8984 (m-30) REVERT: E 415 GLU cc_start: 0.8380 (pm20) cc_final: 0.7656 (mt-10) REVERT: E 420 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8129 (mm-30) REVERT: E 424 ASP cc_start: 0.9139 (m-30) cc_final: 0.8289 (m-30) REVERT: E 430 LYS cc_start: 0.9125 (tppp) cc_final: 0.8553 (tppt) REVERT: F 71 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7659 (mm-30) REVERT: F 163 ASP cc_start: 0.9048 (p0) cc_final: 0.8844 (p0) REVERT: F 259 MET cc_start: 0.8772 (mmm) cc_final: 0.8074 (mmt) REVERT: F 281 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8057 (tm-30) REVERT: F 326 LYS cc_start: 0.9114 (tttt) cc_final: 0.8913 (tptp) REVERT: F 349 ASN cc_start: 0.8283 (t0) cc_final: 0.7884 (t0) REVERT: F 411 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8707 (mm-30) REVERT: F 415 GLU cc_start: 0.8583 (pm20) cc_final: 0.8111 (pm20) REVERT: F 416 MET cc_start: 0.8736 (mmm) cc_final: 0.8271 (mmm) REVERT: F 431 GLU cc_start: 0.8794 (tt0) cc_final: 0.8478 (mt-10) REVERT: J 71 GLU cc_start: 0.7832 (pt0) cc_final: 0.7199 (pt0) REVERT: J 154 MET cc_start: 0.9071 (mmm) cc_final: 0.8568 (mmm) REVERT: J 230 LEU cc_start: 0.9327 (tp) cc_final: 0.9069 (mp) REVERT: J 285 GLN cc_start: 0.8393 (tt0) cc_final: 0.8146 (tt0) REVERT: J 357 TYR cc_start: 0.9006 (m-80) cc_final: 0.8804 (m-80) REVERT: J 377 MET cc_start: 0.9042 (tmm) cc_final: 0.8526 (tmm) REVERT: J 411 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7818 (mm-30) REVERT: J 420 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8561 (mm-30) REVERT: J 423 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8427 (tm-30) REVERT: H 55 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 76 ASP cc_start: 0.8858 (m-30) cc_final: 0.8326 (m-30) REVERT: H 110 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8186 (mt-10) REVERT: H 159 GLU cc_start: 0.9157 (tp30) cc_final: 0.8911 (pt0) REVERT: H 160 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8404 (tp30) REVERT: H 211 ASP cc_start: 0.9061 (m-30) cc_final: 0.8734 (t70) REVERT: H 281 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8338 (tm-30) REVERT: H 352 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8574 (tttp) REVERT: H 386 GLU cc_start: 0.8347 (pt0) cc_final: 0.7656 (pp20) REVERT: H 420 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8753 (mm-30) REVERT: H 431 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8296 (mm-30) REVERT: H 435 TYR cc_start: 0.8781 (m-80) cc_final: 0.8560 (m-80) REVERT: L 24 TYR cc_start: 0.8959 (m-80) cc_final: 0.8491 (m-80) REVERT: L 35 GLN cc_start: 0.8942 (tt0) cc_final: 0.8654 (tp40) REVERT: L 47 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.5801 (m-30) REVERT: L 76 ASP cc_start: 0.8909 (m-30) cc_final: 0.8564 (m-30) REVERT: L 112 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8562 (ptpp) REVERT: L 113 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8187 (mp0) REVERT: L 120 ASP cc_start: 0.9080 (t0) cc_final: 0.8859 (t0) REVERT: L 192 HIS cc_start: 0.9123 (t-90) cc_final: 0.8851 (t-170) REVERT: L 199 ASP cc_start: 0.8935 (m-30) cc_final: 0.8455 (m-30) REVERT: L 269 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8653 (pp) REVERT: L 411 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8120 (mm-30) REVERT: L 415 GLU cc_start: 0.8417 (pm20) cc_final: 0.7825 (mt-10) REVERT: L 430 LYS cc_start: 0.9252 (tppt) cc_final: 0.9004 (tppt) REVERT: L 433 GLU cc_start: 0.9226 (tp30) cc_final: 0.8811 (tp30) REVERT: G 1 MET cc_start: 0.9037 (mmm) cc_final: 0.8732 (mmp) REVERT: G 151 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8696 (m) REVERT: G 160 GLU cc_start: 0.9004 (tp30) cc_final: 0.8597 (tp30) REVERT: G 170 SER cc_start: 0.8421 (m) cc_final: 0.8049 (p) REVERT: G 293 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8539 (pp30) REVERT: G 314 THR cc_start: 0.9281 (m) cc_final: 0.8967 (p) REVERT: G 322 ARG cc_start: 0.9090 (mtp85) cc_final: 0.8889 (mmm160) REVERT: K 112 LYS cc_start: 0.8965 (pttm) cc_final: 0.8479 (pttm) REVERT: K 254 GLU cc_start: 0.4127 (mm-30) cc_final: 0.3498 (mm-30) REVERT: K 293 ASN cc_start: 0.9147 (m-40) cc_final: 0.8666 (m-40) REVERT: K 326 LYS cc_start: 0.6152 (mmtt) cc_final: 0.5342 (pttt) REVERT: K 339 ARG cc_start: 0.8597 (tpp80) cc_final: 0.8274 (tpp-160) REVERT: K 357 TYR cc_start: 0.8886 (m-80) cc_final: 0.8492 (m-80) REVERT: K 411 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8191 (mm-30) REVERT: K 415 GLU cc_start: 0.8234 (pm20) cc_final: 0.7425 (mt-10) REVERT: I 12 CYS cc_start: 0.8613 (t) cc_final: 0.8123 (t) REVERT: I 37 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8460 (m90) REVERT: I 47 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8156 (mm-30) REVERT: I 59 ASN cc_start: 0.8635 (m-40) cc_final: 0.8249 (p0) REVERT: I 71 GLU cc_start: 0.8477 (tp30) cc_final: 0.8127 (tm-30) REVERT: I 205 ASP cc_start: 0.8471 (t0) cc_final: 0.8245 (t0) REVERT: I 211 ASP cc_start: 0.8897 (m-30) cc_final: 0.8352 (t0) REVERT: I 215 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7910 (mtm-85) REVERT: I 278 ARG cc_start: 0.8273 (tpm170) cc_final: 0.7946 (tpm170) REVERT: I 329 ASP cc_start: 0.8257 (m-30) cc_final: 0.7992 (m-30) REVERT: I 386 GLU cc_start: 0.8651 (pt0) cc_final: 0.8367 (pt0) REVERT: I 405 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8967 (tt) REVERT: I 416 MET cc_start: 0.9328 (ttm) cc_final: 0.9080 (ttm) outliers start: 140 outliers final: 86 residues processed: 1112 average time/residue: 0.2361 time to fit residues: 436.7612 Evaluate side-chains 1066 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 965 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 234 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 341 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 405 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 267 optimal weight: 8.9990 chunk 405 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 404 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 429 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 452 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN T 311 GLN T 330 GLN E 101 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** J 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 309 HIS H 349 ASN L 128 GLN K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077131 restraints weight = 71838.543| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.12 r_work: 0.2984 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 42070 Z= 0.123 Angle : 0.564 9.194 57162 Z= 0.291 Chirality : 0.042 0.181 6252 Planarity : 0.004 0.050 7436 Dihedral : 9.887 168.085 5769 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.77 % Allowed : 20.61 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 5160 helix: 1.81 (0.10), residues: 2458 sheet: 1.19 (0.19), residues: 756 loop : -0.59 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 264 TYR 0.012 0.001 TYR E 108 PHE 0.030 0.001 PHE D 20 TRP 0.030 0.002 TRP H 346 HIS 0.016 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (42070) covalent geometry : angle 0.56365 / 0.29 (57162) hydrogen bonds : bond 0.04299 / 2.90 ( 2119) hydrogen bonds : angle 4.46946 / 3.22 ( 6123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1014 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: A 123 ARG cc_start: 0.9043 (tpp80) cc_final: 0.8830 (tpp80) REVERT: A 156 ARG cc_start: 0.9083 (mmt90) cc_final: 0.8673 (mmm-85) REVERT: A 176 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8646 (mm110) REVERT: A 196 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: A 199 ASP cc_start: 0.8892 (m-30) cc_final: 0.8392 (m-30) REVERT: A 415 GLU cc_start: 0.8633 (pm20) cc_final: 0.8084 (mt-10) REVERT: A 430 LYS cc_start: 0.9045 (tppp) cc_final: 0.8659 (tppp) REVERT: B 124 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8703 (tttp) REVERT: B 193 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8366 (mp10) REVERT: B 215 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7710 (mtt90) REVERT: B 259 MET cc_start: 0.8640 (mmp) cc_final: 0.8312 (mmp) REVERT: B 281 GLN cc_start: 0.8842 (tp40) cc_final: 0.8256 (tp40) REVERT: B 308 ARG cc_start: 0.9008 (mpp80) cc_final: 0.8284 (mtm-85) REVERT: B 309 HIS cc_start: 0.9090 (m90) cc_final: 0.8475 (m-70) REVERT: B 349 ASN cc_start: 0.8109 (t0) cc_final: 0.7900 (t0) REVERT: B 400 ARG cc_start: 0.9149 (ttm-80) cc_final: 0.8942 (ttt90) REVERT: B 416 MET cc_start: 0.8807 (mmm) cc_final: 0.8492 (mmm) REVERT: C 47 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: C 90 GLU cc_start: 0.8687 (tt0) cc_final: 0.8396 (tt0) REVERT: C 127 ASP cc_start: 0.8586 (m-30) cc_final: 0.8352 (m-30) REVERT: C 176 GLN cc_start: 0.9337 (mm-40) cc_final: 0.9017 (mm110) REVERT: C 196 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: C 254 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8223 (mt-10) REVERT: C 396 ASP cc_start: 0.9323 (t70) cc_final: 0.9043 (m-30) REVERT: C 411 GLU cc_start: 0.8352 (tp30) cc_final: 0.7732 (mm-30) REVERT: C 420 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8720 (mm-30) REVERT: C 423 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9033 (pp20) REVERT: C 433 GLU cc_start: 0.9178 (tp30) cc_final: 0.8966 (tm-30) REVERT: D 50 ASN cc_start: 0.9172 (p0) cc_final: 0.8854 (p0) REVERT: D 53 TYR cc_start: 0.8984 (m-80) cc_final: 0.8441 (m-80) REVERT: D 71 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8115 (tt0) REVERT: D 113 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8436 (mm-30) REVERT: D 127 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8553 (mp0) REVERT: D 166 MET cc_start: 0.9136 (tpp) cc_final: 0.8915 (tpt) REVERT: D 205 ASP cc_start: 0.8738 (t0) cc_final: 0.7934 (t70) REVERT: D 209 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 240 THR cc_start: 0.8527 (m) cc_final: 0.8177 (m) REVERT: D 259 MET cc_start: 0.8611 (mmp) cc_final: 0.7886 (mmt) REVERT: D 278 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8324 (tpm170) REVERT: D 281 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8361 (tm-30) REVERT: D 284 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7524 (ptm160) REVERT: D 290 GLU cc_start: 0.8569 (tt0) cc_final: 0.8237 (tt0) REVERT: D 293 GLN cc_start: 0.8914 (pt0) cc_final: 0.8629 (pp30) REVERT: D 309 HIS cc_start: 0.9235 (m90) cc_final: 0.8369 (m-70) REVERT: D 416 MET cc_start: 0.8770 (mmm) cc_final: 0.8555 (mmm) REVERT: D 431 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7957 (mm-30) REVERT: E 47 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.5586 (t70) REVERT: E 91 GLN cc_start: 0.8830 (mt0) cc_final: 0.8423 (mp10) REVERT: E 254 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7802 (mt-10) REVERT: E 285 GLN cc_start: 0.8401 (tt0) cc_final: 0.8159 (pt0) REVERT: E 313 MET cc_start: 0.9373 (mtm) cc_final: 0.8506 (mtm) REVERT: E 380 ASN cc_start: 0.9011 (t0) cc_final: 0.7931 (t0) REVERT: E 396 ASP cc_start: 0.9217 (t70) cc_final: 0.8967 (m-30) REVERT: E 415 GLU cc_start: 0.8338 (pm20) cc_final: 0.7655 (mt-10) REVERT: E 420 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8528 (mm-30) REVERT: E 424 ASP cc_start: 0.9037 (m-30) cc_final: 0.8582 (m-30) REVERT: E 430 LYS cc_start: 0.9138 (tppp) cc_final: 0.8589 (tppt) REVERT: F 3 GLU cc_start: 0.8340 (mp0) cc_final: 0.7792 (mp0) REVERT: F 71 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7794 (mm-30) REVERT: F 163 ASP cc_start: 0.9006 (p0) cc_final: 0.8767 (p0) REVERT: F 326 LYS cc_start: 0.9077 (tttt) cc_final: 0.8874 (tptp) REVERT: F 349 ASN cc_start: 0.8191 (t0) cc_final: 0.7790 (t0) REVERT: F 415 GLU cc_start: 0.8599 (pm20) cc_final: 0.8227 (pm20) REVERT: F 416 MET cc_start: 0.8749 (mmm) cc_final: 0.8386 (mmm) REVERT: F 431 GLU cc_start: 0.8800 (tt0) cc_final: 0.8449 (mt-10) REVERT: J 71 GLU cc_start: 0.7733 (pt0) cc_final: 0.7255 (pt0) REVERT: J 112 LYS cc_start: 0.8808 (ptpp) cc_final: 0.8587 (pttm) REVERT: J 154 MET cc_start: 0.9093 (mmm) cc_final: 0.8665 (mmm) REVERT: J 213 CYS cc_start: 0.9086 (m) cc_final: 0.8620 (m) REVERT: J 230 LEU cc_start: 0.9301 (tp) cc_final: 0.8992 (mp) REVERT: J 254 GLU cc_start: 0.3631 (mm-30) cc_final: 0.3316 (mm-30) REVERT: J 411 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7873 (mm-30) REVERT: J 413 MET cc_start: 0.7891 (tpp) cc_final: 0.7252 (tpp) REVERT: J 420 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8625 (mm-30) REVERT: J 423 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8422 (tm-30) REVERT: J 432 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7033 (t80) REVERT: H 55 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7543 (tm-30) REVERT: H 76 ASP cc_start: 0.8889 (m-30) cc_final: 0.8356 (m-30) REVERT: H 110 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8291 (mt-10) REVERT: H 183 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7863 (mt-10) REVERT: H 205 ASP cc_start: 0.8599 (t0) cc_final: 0.8285 (t0) REVERT: H 211 ASP cc_start: 0.9064 (m-30) cc_final: 0.8726 (t70) REVERT: H 215 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7186 (mtp180) REVERT: H 281 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8328 (tm-30) REVERT: H 352 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8508 (tttp) REVERT: H 420 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8763 (mm-30) REVERT: H 431 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8139 (mm-30) REVERT: L 35 GLN cc_start: 0.8973 (tt0) cc_final: 0.8697 (tp40) REVERT: L 47 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6327 (m-30) REVERT: L 69 ASP cc_start: 0.8520 (t0) cc_final: 0.8224 (t0) REVERT: L 71 GLU cc_start: 0.7784 (pt0) cc_final: 0.7123 (pt0) REVERT: L 76 ASP cc_start: 0.8949 (m-30) cc_final: 0.8589 (m-30) REVERT: L 112 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8516 (ptpp) REVERT: L 113 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8240 (mp0) REVERT: L 120 ASP cc_start: 0.9089 (t0) cc_final: 0.8870 (t0) REVERT: L 199 ASP cc_start: 0.8953 (m-30) cc_final: 0.8493 (m-30) REVERT: L 269 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8774 (pp) REVERT: L 306 ASP cc_start: 0.9079 (t0) cc_final: 0.8846 (p0) REVERT: L 411 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8156 (mm-30) REVERT: L 415 GLU cc_start: 0.8416 (pm20) cc_final: 0.7823 (mt-10) REVERT: L 430 LYS cc_start: 0.9268 (tppt) cc_final: 0.9019 (tppt) REVERT: L 433 GLU cc_start: 0.9166 (tp30) cc_final: 0.8743 (tp30) REVERT: G 1 MET cc_start: 0.8999 (mmm) cc_final: 0.8660 (mmp) REVERT: G 75 MET cc_start: 0.8759 (mmm) cc_final: 0.8466 (mmt) REVERT: G 151 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8690 (m) REVERT: G 160 GLU cc_start: 0.9009 (tp30) cc_final: 0.8593 (tp30) REVERT: G 170 SER cc_start: 0.8428 (m) cc_final: 0.8105 (p) REVERT: G 290 GLU cc_start: 0.8576 (tt0) cc_final: 0.8272 (tt0) REVERT: G 293 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8555 (pp30) REVERT: G 314 THR cc_start: 0.9278 (m) cc_final: 0.8944 (p) REVERT: K 76 ASP cc_start: 0.8839 (m-30) cc_final: 0.8247 (m-30) REVERT: K 112 LYS cc_start: 0.8963 (pttm) cc_final: 0.8473 (pttm) REVERT: K 293 ASN cc_start: 0.9091 (m-40) cc_final: 0.8604 (m-40) REVERT: K 326 LYS cc_start: 0.6095 (mmtt) cc_final: 0.5344 (pttt) REVERT: K 339 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8178 (tpp-160) REVERT: K 357 TYR cc_start: 0.8919 (m-80) cc_final: 0.8507 (m-80) REVERT: K 411 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7919 (mm-30) REVERT: K 415 GLU cc_start: 0.8193 (pm20) cc_final: 0.7369 (mt-10) REVERT: K 423 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8308 (mt-10) REVERT: I 12 CYS cc_start: 0.8554 (t) cc_final: 0.8050 (t) REVERT: I 37 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8564 (m90) REVERT: I 47 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8124 (mm-30) REVERT: I 59 ASN cc_start: 0.8578 (m-40) cc_final: 0.8240 (p0) REVERT: I 69 ASP cc_start: 0.8065 (t0) cc_final: 0.7743 (t0) REVERT: I 71 GLU cc_start: 0.8396 (tp30) cc_final: 0.7731 (tm-30) REVERT: I 205 ASP cc_start: 0.8434 (t0) cc_final: 0.8077 (t0) REVERT: I 211 ASP cc_start: 0.8885 (m-30) cc_final: 0.8455 (t0) REVERT: I 269 MET cc_start: 0.8993 (mtp) cc_final: 0.8745 (mtt) REVERT: I 278 ARG cc_start: 0.8278 (tpm170) cc_final: 0.7946 (tpm170) REVERT: I 309 HIS cc_start: 0.9344 (m90) cc_final: 0.9040 (m90) REVERT: I 386 GLU cc_start: 0.8568 (pt0) cc_final: 0.8261 (pt0) REVERT: I 405 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8956 (tt) REVERT: I 417 GLU cc_start: 0.8871 (mp0) cc_final: 0.8600 (mp0) outliers start: 122 outliers final: 87 residues processed: 1080 average time/residue: 0.2341 time to fit residues: 421.1136 Evaluate side-chains 1069 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 969 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 405 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 515 optimal weight: 2.9990 chunk 501 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 465 optimal weight: 0.9990 chunk 399 optimal weight: 6.9990 chunk 271 optimal weight: 0.8980 chunk 380 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN T 311 GLN E 309 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 349 ASN L 192 HIS G 28 HIS K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077409 restraints weight = 72180.108| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.17 r_work: 0.2987 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42070 Z= 0.125 Angle : 0.571 9.231 57162 Z= 0.295 Chirality : 0.042 0.267 6252 Planarity : 0.004 0.054 7436 Dihedral : 9.702 163.992 5767 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.95 % Allowed : 20.66 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.12), residues: 5160 helix: 1.78 (0.11), residues: 2458 sheet: 1.12 (0.20), residues: 750 loop : -0.62 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 278 TYR 0.016 0.001 TYR C 319 PHE 0.033 0.001 PHE D 20 TRP 0.032 0.002 TRP H 346 HIS 0.009 0.001 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (42070) covalent geometry : angle 0.57071 / 0.29 (57162) hydrogen bonds : bond 0.04258 / 2.87 ( 2119) hydrogen bonds : angle 4.46661 / 3.22 ( 6123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1000 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: A 123 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8830 (tpp80) REVERT: A 156 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8553 (mmm-85) REVERT: A 168 GLU cc_start: 0.8471 (pt0) cc_final: 0.8173 (pt0) REVERT: A 199 ASP cc_start: 0.8874 (m-30) cc_final: 0.8380 (m-30) REVERT: A 415 GLU cc_start: 0.8680 (pm20) cc_final: 0.8081 (mt-10) REVERT: A 430 LYS cc_start: 0.9021 (tppp) cc_final: 0.8640 (tppp) REVERT: B 193 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8273 (mp10) REVERT: B 215 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7583 (mtt90) REVERT: B 259 MET cc_start: 0.8579 (mmp) cc_final: 0.8269 (mmp) REVERT: B 281 GLN cc_start: 0.8777 (tp40) cc_final: 0.8309 (tp-100) REVERT: B 308 ARG cc_start: 0.8971 (mpp80) cc_final: 0.8336 (mtm-85) REVERT: B 309 HIS cc_start: 0.9047 (m90) cc_final: 0.8435 (m-70) REVERT: B 349 ASN cc_start: 0.7961 (t0) cc_final: 0.7657 (t0) REVERT: B 400 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8939 (ttt90) REVERT: B 415 GLU cc_start: 0.8711 (pm20) cc_final: 0.8070 (pm20) REVERT: B 416 MET cc_start: 0.8853 (mmm) cc_final: 0.7997 (mmm) REVERT: B 431 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8412 (mt-10) REVERT: C 47 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6107 (m-30) REVERT: C 90 GLU cc_start: 0.8700 (tt0) cc_final: 0.8391 (tt0) REVERT: C 127 ASP cc_start: 0.8593 (m-30) cc_final: 0.8354 (m-30) REVERT: C 176 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9021 (mm110) REVERT: C 196 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: C 254 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 313 MET cc_start: 0.9216 (mtm) cc_final: 0.8654 (mtm) REVERT: C 377 MET cc_start: 0.9145 (tmm) cc_final: 0.8903 (tmm) REVERT: C 411 GLU cc_start: 0.8373 (tp30) cc_final: 0.7771 (mm-30) REVERT: D 50 ASN cc_start: 0.9232 (p0) cc_final: 0.8922 (p0) REVERT: D 53 TYR cc_start: 0.8971 (m-80) cc_final: 0.8397 (m-80) REVERT: D 127 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8505 (mp0) REVERT: D 166 MET cc_start: 0.9145 (tpp) cc_final: 0.8937 (tpt) REVERT: D 209 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8885 (mp) REVERT: D 240 THR cc_start: 0.8486 (m) cc_final: 0.8132 (m) REVERT: D 259 MET cc_start: 0.8550 (mmp) cc_final: 0.7829 (mmt) REVERT: D 278 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8360 (tpm170) REVERT: D 281 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 284 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7486 (ptm160) REVERT: D 290 GLU cc_start: 0.8680 (tt0) cc_final: 0.8333 (tt0) REVERT: D 293 GLN cc_start: 0.8947 (pt0) cc_final: 0.8638 (pp30) REVERT: D 415 GLU cc_start: 0.8811 (pm20) cc_final: 0.8512 (pm20) REVERT: D 416 MET cc_start: 0.8743 (mmm) cc_final: 0.8489 (mmm) REVERT: D 431 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: E 47 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: E 91 GLN cc_start: 0.8808 (mt0) cc_final: 0.8414 (mp10) REVERT: E 254 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7724 (mt-10) REVERT: E 275 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (m) REVERT: E 313 MET cc_start: 0.9373 (mtm) cc_final: 0.8555 (mtm) REVERT: E 380 ASN cc_start: 0.9010 (t0) cc_final: 0.8079 (t0) REVERT: E 396 ASP cc_start: 0.9212 (OUTLIER) cc_final: 0.8959 (m-30) REVERT: E 415 GLU cc_start: 0.8286 (pm20) cc_final: 0.7626 (mt-10) REVERT: E 424 ASP cc_start: 0.9056 (m-30) cc_final: 0.8626 (m-30) REVERT: E 430 LYS cc_start: 0.9123 (tppp) cc_final: 0.8568 (tppt) REVERT: F 3 GLU cc_start: 0.8303 (mp0) cc_final: 0.7728 (mp0) REVERT: F 71 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7797 (mm-30) REVERT: F 141 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8735 (mt) REVERT: F 163 ASP cc_start: 0.8997 (p0) cc_final: 0.8760 (p0) REVERT: F 259 MET cc_start: 0.8848 (mmm) cc_final: 0.8324 (mmt) REVERT: F 349 ASN cc_start: 0.8227 (t0) cc_final: 0.7840 (t0) REVERT: F 386 GLU cc_start: 0.8745 (pt0) cc_final: 0.8371 (pp20) REVERT: F 415 GLU cc_start: 0.8530 (pm20) cc_final: 0.8166 (pm20) REVERT: F 416 MET cc_start: 0.8734 (mmm) cc_final: 0.8366 (mmm) REVERT: F 431 GLU cc_start: 0.8747 (tt0) cc_final: 0.8389 (mt-10) REVERT: J 71 GLU cc_start: 0.7706 (pt0) cc_final: 0.7474 (pt0) REVERT: J 112 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8635 (pttm) REVERT: J 154 MET cc_start: 0.9073 (mmm) cc_final: 0.8658 (mmm) REVERT: J 213 CYS cc_start: 0.9074 (m) cc_final: 0.8616 (m) REVERT: J 230 LEU cc_start: 0.9342 (tp) cc_final: 0.9046 (mp) REVERT: J 254 GLU cc_start: 0.3633 (mm-30) cc_final: 0.3317 (mm-30) REVERT: J 357 TYR cc_start: 0.8922 (m-80) cc_final: 0.8536 (m-80) REVERT: J 377 MET cc_start: 0.8941 (tmm) cc_final: 0.8454 (tmm) REVERT: J 411 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7856 (mm-30) REVERT: J 413 MET cc_start: 0.7860 (tpp) cc_final: 0.7264 (tpp) REVERT: J 420 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8522 (mm-30) REVERT: J 423 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8381 (tm-30) REVERT: J 432 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7126 (t80) REVERT: H 55 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7485 (tm-30) REVERT: H 76 ASP cc_start: 0.8864 (m-30) cc_final: 0.8316 (m-30) REVERT: H 110 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8518 (mm-30) REVERT: H 160 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8318 (tp30) REVERT: H 183 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7835 (mt-10) REVERT: H 205 ASP cc_start: 0.8598 (t0) cc_final: 0.8318 (t0) REVERT: H 211 ASP cc_start: 0.9051 (m-30) cc_final: 0.8797 (t70) REVERT: H 215 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7150 (mtp180) REVERT: H 352 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8489 (tttp) REVERT: H 420 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8773 (mm-30) REVERT: H 431 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8088 (mm-30) REVERT: L 35 GLN cc_start: 0.8957 (tt0) cc_final: 0.8674 (tp40) REVERT: L 47 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.5986 (m-30) REVERT: L 69 ASP cc_start: 0.8626 (t0) cc_final: 0.8318 (t0) REVERT: L 71 GLU cc_start: 0.7755 (pt0) cc_final: 0.7038 (pt0) REVERT: L 76 ASP cc_start: 0.8951 (m-30) cc_final: 0.8582 (m-30) REVERT: L 112 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8503 (ptpp) REVERT: L 113 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8203 (mp0) REVERT: L 120 ASP cc_start: 0.9065 (t0) cc_final: 0.8836 (t0) REVERT: L 199 ASP cc_start: 0.8970 (m-30) cc_final: 0.8510 (m-30) REVERT: L 269 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8746 (pp) REVERT: L 411 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8061 (mm-30) REVERT: L 415 GLU cc_start: 0.8376 (pm20) cc_final: 0.7830 (mt-10) REVERT: L 423 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8087 (mt-10) REVERT: L 430 LYS cc_start: 0.9258 (tppt) cc_final: 0.9011 (tppt) REVERT: L 433 GLU cc_start: 0.9176 (tp30) cc_final: 0.8796 (tp30) REVERT: G 1 MET cc_start: 0.9084 (mmm) cc_final: 0.8534 (mmp) REVERT: G 151 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8701 (m) REVERT: G 160 GLU cc_start: 0.9021 (tp30) cc_final: 0.8613 (tp30) REVERT: G 170 SER cc_start: 0.8388 (m) cc_final: 0.8057 (p) REVERT: G 290 GLU cc_start: 0.8553 (tt0) cc_final: 0.8248 (tt0) REVERT: G 293 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8542 (pp30) REVERT: G 309 HIS cc_start: 0.9433 (m90) cc_final: 0.9160 (m90) REVERT: G 314 THR cc_start: 0.9287 (m) cc_final: 0.8915 (p) REVERT: K 71 GLU cc_start: 0.8069 (pt0) cc_final: 0.7735 (tt0) REVERT: K 112 LYS cc_start: 0.8933 (pttm) cc_final: 0.8346 (pttm) REVERT: K 176 GLN cc_start: 0.9112 (mm110) cc_final: 0.8819 (mm110) REVERT: K 254 GLU cc_start: 0.4551 (mm-30) cc_final: 0.3916 (mm-30) REVERT: K 293 ASN cc_start: 0.9090 (m-40) cc_final: 0.8599 (m-40) REVERT: K 326 LYS cc_start: 0.6151 (mmtt) cc_final: 0.5327 (pttt) REVERT: K 339 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8291 (tpp-160) REVERT: K 342 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8631 (tt0) REVERT: K 357 TYR cc_start: 0.8955 (m-80) cc_final: 0.8520 (m-80) REVERT: K 411 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7898 (mm-30) REVERT: K 423 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8267 (mt-10) REVERT: I 12 CYS cc_start: 0.8581 (t) cc_final: 0.8057 (t) REVERT: I 47 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8279 (mm-30) REVERT: I 59 ASN cc_start: 0.8669 (m-40) cc_final: 0.8300 (p0) REVERT: I 69 ASP cc_start: 0.8044 (t0) cc_final: 0.7721 (t0) REVERT: I 71 GLU cc_start: 0.8416 (tp30) cc_final: 0.7764 (tm-30) REVERT: I 205 ASP cc_start: 0.8474 (t0) cc_final: 0.8108 (t0) REVERT: I 211 ASP cc_start: 0.8916 (m-30) cc_final: 0.8488 (t0) REVERT: I 278 ARG cc_start: 0.8254 (tpm170) cc_final: 0.7917 (tpm170) REVERT: I 309 HIS cc_start: 0.9343 (m90) cc_final: 0.8995 (m90) REVERT: I 386 GLU cc_start: 0.8632 (pt0) cc_final: 0.8309 (pt0) REVERT: I 405 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8973 (tt) REVERT: I 417 GLU cc_start: 0.8863 (mp0) cc_final: 0.8582 (mp0) REVERT: P 338 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7401 (t) outliers start: 130 outliers final: 98 residues processed: 1068 average time/residue: 0.2374 time to fit residues: 423.2511 Evaluate side-chains 1088 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 973 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain P residue 307 PHE Chi-restraints excluded: chain P residue 338 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 196 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 386 optimal weight: 0.8980 chunk 438 optimal weight: 0.9980 chunk 407 optimal weight: 0.8980 chunk 451 optimal weight: 0.7980 chunk 354 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN T 311 GLN E 309 HIS F 6 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 136 GLN H 349 ASN L 192 HIS K 192 HIS K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077548 restraints weight = 71743.600| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.14 r_work: 0.2998 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 42070 Z= 0.128 Angle : 0.583 9.553 57162 Z= 0.302 Chirality : 0.043 0.223 6252 Planarity : 0.004 0.057 7436 Dihedral : 9.551 159.846 5767 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.79 % Allowed : 21.11 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.12), residues: 5160 helix: 1.74 (0.11), residues: 2458 sheet: 1.12 (0.20), residues: 750 loop : -0.61 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 278 TYR 0.017 0.001 TYR J 172 PHE 0.035 0.001 PHE D 20 TRP 0.026 0.002 TRP I 346 HIS 0.028 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (42070) covalent geometry : angle 0.58349 / 0.30 (57162) hydrogen bonds : bond 0.04227 / 2.85 ( 2119) hydrogen bonds : angle 4.47127 / 3.23 ( 6123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 993 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.9140 (tpp80) cc_final: 0.8830 (tpp80) REVERT: A 168 GLU cc_start: 0.8369 (pt0) cc_final: 0.8078 (pt0) REVERT: A 196 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 199 ASP cc_start: 0.8793 (m-30) cc_final: 0.8327 (m-30) REVERT: A 411 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7735 (tp30) REVERT: A 415 GLU cc_start: 0.8717 (pm20) cc_final: 0.8120 (mt-10) REVERT: A 430 LYS cc_start: 0.9093 (tppp) cc_final: 0.8739 (tppp) REVERT: B 124 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8696 (tttp) REVERT: B 193 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8286 (mp10) REVERT: B 215 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7654 (mtt90) REVERT: B 259 MET cc_start: 0.8722 (mmp) cc_final: 0.8499 (mmp) REVERT: B 281 GLN cc_start: 0.8827 (tp40) cc_final: 0.8401 (tp-100) REVERT: B 308 ARG cc_start: 0.8995 (mpp80) cc_final: 0.8332 (mtm-85) REVERT: B 309 HIS cc_start: 0.9094 (m90) cc_final: 0.8529 (m-70) REVERT: B 333 LEU cc_start: 0.9585 (tp) cc_final: 0.9261 (tp) REVERT: B 349 ASN cc_start: 0.8052 (t0) cc_final: 0.7717 (t0) REVERT: B 400 ARG cc_start: 0.9118 (ttm-80) cc_final: 0.8884 (ttt90) REVERT: B 415 GLU cc_start: 0.8696 (pm20) cc_final: 0.8052 (pm20) REVERT: B 416 MET cc_start: 0.8836 (mmm) cc_final: 0.7944 (mmm) REVERT: B 431 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8365 (mt-10) REVERT: C 47 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: C 90 GLU cc_start: 0.8744 (tt0) cc_final: 0.8415 (tt0) REVERT: C 127 ASP cc_start: 0.8632 (m-30) cc_final: 0.8407 (m-30) REVERT: C 176 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8979 (mm110) REVERT: C 196 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: C 313 MET cc_start: 0.9131 (mtm) cc_final: 0.8527 (mtm) REVERT: C 377 MET cc_start: 0.9122 (tmm) cc_final: 0.8837 (tmm) REVERT: D 50 ASN cc_start: 0.9218 (p0) cc_final: 0.8910 (p0) REVERT: D 127 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8590 (mp0) REVERT: D 166 MET cc_start: 0.9095 (tpp) cc_final: 0.8880 (tpt) REVERT: D 209 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8933 (mp) REVERT: D 240 THR cc_start: 0.8476 (m) cc_final: 0.8124 (m) REVERT: D 259 MET cc_start: 0.8487 (mmp) cc_final: 0.7744 (mmt) REVERT: D 278 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8294 (tpm170) REVERT: D 281 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8372 (tm-30) REVERT: D 284 ARG cc_start: 0.7838 (ptm160) cc_final: 0.7556 (ptm160) REVERT: D 290 GLU cc_start: 0.8527 (tt0) cc_final: 0.8186 (tt0) REVERT: D 293 GLN cc_start: 0.8922 (pt0) cc_final: 0.8604 (pp30) REVERT: D 427 ASP cc_start: 0.9156 (m-30) cc_final: 0.8458 (m-30) REVERT: D 431 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: E 47 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.5360 (m-30) REVERT: E 91 GLN cc_start: 0.8799 (mt0) cc_final: 0.8433 (mp10) REVERT: E 254 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7790 (mt-10) REVERT: E 275 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8737 (m) REVERT: E 313 MET cc_start: 0.9331 (mtm) cc_final: 0.8499 (mtm) REVERT: E 357 TYR cc_start: 0.9066 (m-80) cc_final: 0.8773 (m-80) REVERT: E 380 ASN cc_start: 0.8985 (t0) cc_final: 0.8016 (t0) REVERT: E 411 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7698 (tp30) REVERT: E 415 GLU cc_start: 0.8247 (pm20) cc_final: 0.7592 (mt-10) REVERT: E 424 ASP cc_start: 0.9027 (m-30) cc_final: 0.8593 (m-30) REVERT: E 430 LYS cc_start: 0.9155 (tppp) cc_final: 0.8607 (tppt) REVERT: F 71 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7790 (mm-30) REVERT: F 141 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8771 (mt) REVERT: F 163 ASP cc_start: 0.9027 (p0) cc_final: 0.8793 (p0) REVERT: F 259 MET cc_start: 0.8853 (mmm) cc_final: 0.8393 (mmt) REVERT: F 349 ASN cc_start: 0.8361 (t0) cc_final: 0.7940 (t0) REVERT: F 386 GLU cc_start: 0.8695 (pt0) cc_final: 0.8288 (pp20) REVERT: F 415 GLU cc_start: 0.8526 (pm20) cc_final: 0.8152 (pm20) REVERT: F 416 MET cc_start: 0.8722 (mmm) cc_final: 0.8440 (mmm) REVERT: F 431 GLU cc_start: 0.8779 (tt0) cc_final: 0.8429 (mt-10) REVERT: J 112 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8587 (pttm) REVERT: J 154 MET cc_start: 0.8999 (mmm) cc_final: 0.8595 (mmm) REVERT: J 230 LEU cc_start: 0.9285 (tp) cc_final: 0.9040 (mm) REVERT: J 254 GLU cc_start: 0.3617 (mm-30) cc_final: 0.3172 (mm-30) REVERT: J 357 TYR cc_start: 0.8968 (m-80) cc_final: 0.8587 (m-80) REVERT: J 411 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7926 (mm-30) REVERT: J 413 MET cc_start: 0.7868 (tpp) cc_final: 0.7240 (tpp) REVERT: J 432 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7279 (t80) REVERT: H 55 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7457 (tm-30) REVERT: H 76 ASP cc_start: 0.8959 (m-30) cc_final: 0.8430 (m-30) REVERT: H 110 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8433 (mm-30) REVERT: H 183 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7844 (mt-10) REVERT: H 205 ASP cc_start: 0.8622 (t0) cc_final: 0.8341 (t0) REVERT: H 211 ASP cc_start: 0.9090 (m-30) cc_final: 0.8776 (t70) REVERT: H 215 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7150 (mtp180) REVERT: H 352 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (tttp) REVERT: H 420 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8779 (mm-30) REVERT: H 431 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8084 (mm-30) REVERT: L 35 GLN cc_start: 0.8955 (tt0) cc_final: 0.8686 (tp40) REVERT: L 47 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6064 (m-30) REVERT: L 69 ASP cc_start: 0.8654 (t0) cc_final: 0.8339 (t0) REVERT: L 71 GLU cc_start: 0.7741 (pt0) cc_final: 0.7005 (pt0) REVERT: L 76 ASP cc_start: 0.8937 (m-30) cc_final: 0.8574 (m-30) REVERT: L 112 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8485 (ptpp) REVERT: L 113 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8163 (mp0) REVERT: L 120 ASP cc_start: 0.9062 (t0) cc_final: 0.8832 (t0) REVERT: L 199 ASP cc_start: 0.8905 (m-30) cc_final: 0.8449 (m-30) REVERT: L 259 LEU cc_start: 0.9385 (tt) cc_final: 0.8892 (mt) REVERT: L 269 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8828 (pp) REVERT: L 411 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8150 (mm-30) REVERT: L 415 GLU cc_start: 0.8422 (pm20) cc_final: 0.7864 (mt-10) REVERT: L 423 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8110 (mt-10) REVERT: L 430 LYS cc_start: 0.9256 (tppt) cc_final: 0.9009 (tppt) REVERT: L 433 GLU cc_start: 0.9189 (tp30) cc_final: 0.8816 (tp30) REVERT: G 1 MET cc_start: 0.9050 (mmm) cc_final: 0.8487 (mmp) REVERT: G 151 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8674 (m) REVERT: G 160 GLU cc_start: 0.9031 (tp30) cc_final: 0.8641 (tp30) REVERT: G 170 SER cc_start: 0.8293 (m) cc_final: 0.7969 (p) REVERT: G 290 GLU cc_start: 0.8612 (tt0) cc_final: 0.8140 (tt0) REVERT: G 293 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8533 (pp30) REVERT: G 314 THR cc_start: 0.9288 (m) cc_final: 0.8911 (p) REVERT: K 112 LYS cc_start: 0.8853 (pttm) cc_final: 0.8402 (pttm) REVERT: K 168 GLU cc_start: 0.8506 (pt0) cc_final: 0.8169 (pt0) REVERT: K 176 GLN cc_start: 0.9062 (mm110) cc_final: 0.8668 (mm110) REVERT: K 254 GLU cc_start: 0.4450 (mm-30) cc_final: 0.3518 (mm-30) REVERT: K 293 ASN cc_start: 0.9124 (m-40) cc_final: 0.8607 (m-40) REVERT: K 308 ARG cc_start: 0.9188 (mpp80) cc_final: 0.8929 (mpp80) REVERT: K 326 LYS cc_start: 0.6208 (mmtt) cc_final: 0.5316 (pttt) REVERT: K 339 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8201 (tpp-160) REVERT: K 342 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: K 357 TYR cc_start: 0.9016 (m-80) cc_final: 0.8578 (m-80) REVERT: K 411 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7871 (mm-30) REVERT: K 423 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8187 (mt-10) REVERT: I 12 CYS cc_start: 0.8553 (t) cc_final: 0.8028 (t) REVERT: I 47 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8220 (mm-30) REVERT: I 59 ASN cc_start: 0.8574 (m-40) cc_final: 0.8245 (p0) REVERT: I 69 ASP cc_start: 0.8047 (t0) cc_final: 0.7714 (t0) REVERT: I 71 GLU cc_start: 0.8364 (tp30) cc_final: 0.7699 (tm-30) REVERT: I 205 ASP cc_start: 0.8418 (t0) cc_final: 0.8068 (t0) REVERT: I 211 ASP cc_start: 0.8925 (m-30) cc_final: 0.8367 (t0) REVERT: I 215 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.7907 (mtm-85) REVERT: I 278 ARG cc_start: 0.8188 (tpm170) cc_final: 0.7852 (tpm170) REVERT: I 309 HIS cc_start: 0.9318 (m90) cc_final: 0.8961 (m90) REVERT: I 386 GLU cc_start: 0.8597 (pt0) cc_final: 0.8261 (pt0) REVERT: I 405 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8934 (tt) REVERT: P 338 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7436 (t) outliers start: 123 outliers final: 99 residues processed: 1055 average time/residue: 0.2420 time to fit residues: 425.0416 Evaluate side-chains 1077 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 962 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 309 HIS Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain P residue 307 PHE Chi-restraints excluded: chain P residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 50 optimal weight: 3.9990 chunk 497 optimal weight: 4.9990 chunk 424 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 314 optimal weight: 8.9990 chunk 260 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 356 optimal weight: 10.0000 chunk 396 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN T 311 GLN F 6 HIS F 281 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 136 GLN ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN L 192 HIS G 309 HIS K 192 HIS K 342 GLN K 380 ASN I 6 HIS I 37 HIS I 336 GLN I 349 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075716 restraints weight = 72752.609| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.18 r_work: 0.2955 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 42070 Z= 0.180 Angle : 0.614 10.028 57162 Z= 0.318 Chirality : 0.044 0.246 6252 Planarity : 0.004 0.059 7436 Dihedral : 9.465 155.976 5764 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 21.32 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5160 helix: 1.74 (0.11), residues: 2452 sheet: 1.03 (0.19), residues: 786 loop : -0.57 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 278 TYR 0.017 0.001 TYR J 172 PHE 0.033 0.001 PHE D 20 TRP 0.024 0.002 TRP I 346 HIS 0.033 0.001 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (42070) covalent geometry : angle 0.61383 / 0.32 (57162) hydrogen bonds : bond 0.04653 / 3.14 ( 2119) hydrogen bonds : angle 4.54047 / 3.28 ( 6123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 938 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8832 (tpp80) REVERT: A 168 GLU cc_start: 0.8476 (pt0) cc_final: 0.8144 (pt0) REVERT: A 196 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: A 411 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7944 (tp30) REVERT: A 415 GLU cc_start: 0.8732 (pm20) cc_final: 0.8197 (mt-10) REVERT: A 430 LYS cc_start: 0.9046 (tppp) cc_final: 0.8690 (tppp) REVERT: B 124 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8660 (tttp) REVERT: B 193 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8303 (mp10) REVERT: B 215 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7637 (mtt90) REVERT: B 259 MET cc_start: 0.8610 (mmp) cc_final: 0.8270 (mmp) REVERT: B 308 ARG cc_start: 0.8993 (mpp80) cc_final: 0.8304 (mtm-85) REVERT: B 309 HIS cc_start: 0.9056 (m90) cc_final: 0.8634 (m-70) REVERT: B 333 LEU cc_start: 0.9585 (tp) cc_final: 0.9270 (tp) REVERT: B 349 ASN cc_start: 0.8012 (t0) cc_final: 0.7740 (t0) REVERT: B 386 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8196 (pt0) REVERT: B 400 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8909 (ttt90) REVERT: B 413 MET cc_start: 0.8326 (mtt) cc_final: 0.8055 (mtt) REVERT: B 415 GLU cc_start: 0.8710 (pm20) cc_final: 0.8241 (pm20) REVERT: B 416 MET cc_start: 0.8891 (mmm) cc_final: 0.8212 (mmm) REVERT: C 47 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: C 90 GLU cc_start: 0.8786 (tt0) cc_final: 0.8442 (tt0) REVERT: C 127 ASP cc_start: 0.8639 (m-30) cc_final: 0.8388 (m-30) REVERT: C 176 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8923 (mm110) REVERT: C 196 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: C 313 MET cc_start: 0.9204 (mtm) cc_final: 0.8522 (mtm) REVERT: C 430 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9008 (tppt) REVERT: D 50 ASN cc_start: 0.9279 (p0) cc_final: 0.8982 (p0) REVERT: D 127 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8533 (mp0) REVERT: D 166 MET cc_start: 0.9182 (tpp) cc_final: 0.8938 (tpt) REVERT: D 209 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8977 (mp) REVERT: D 240 THR cc_start: 0.8565 (m) cc_final: 0.8258 (m) REVERT: D 259 MET cc_start: 0.8682 (mmp) cc_final: 0.7997 (mmt) REVERT: D 278 ARG cc_start: 0.8774 (mmm160) cc_final: 0.8440 (tpm170) REVERT: D 281 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 284 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7517 (ptm160) REVERT: D 431 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: E 47 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.5977 (m-30) REVERT: E 76 ASP cc_start: 0.8776 (m-30) cc_final: 0.8265 (m-30) REVERT: E 91 GLN cc_start: 0.8890 (mt0) cc_final: 0.8528 (mt0) REVERT: E 254 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7748 (mt-10) REVERT: E 275 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8736 (m) REVERT: E 313 MET cc_start: 0.9350 (mtm) cc_final: 0.8201 (mtm) REVERT: E 357 TYR cc_start: 0.9103 (m-80) cc_final: 0.8779 (m-80) REVERT: E 411 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7817 (tp30) REVERT: E 415 GLU cc_start: 0.8292 (pm20) cc_final: 0.7633 (mt-10) REVERT: E 424 ASP cc_start: 0.9095 (m-30) cc_final: 0.8696 (m-30) REVERT: E 430 LYS cc_start: 0.9130 (tppp) cc_final: 0.8575 (tppt) REVERT: F 71 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7778 (mm-30) REVERT: F 141 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8800 (mt) REVERT: F 259 MET cc_start: 0.8846 (mmm) cc_final: 0.8384 (mmt) REVERT: F 349 ASN cc_start: 0.8389 (t0) cc_final: 0.7991 (t0) REVERT: F 386 GLU cc_start: 0.8691 (pt0) cc_final: 0.8485 (pp20) REVERT: F 390 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8819 (ptp-170) REVERT: F 415 GLU cc_start: 0.8571 (pm20) cc_final: 0.8216 (pm20) REVERT: F 416 MET cc_start: 0.8795 (mmm) cc_final: 0.8506 (mmm) REVERT: F 431 GLU cc_start: 0.8742 (tt0) cc_final: 0.8380 (mt-10) REVERT: J 112 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8689 (pttm) REVERT: J 154 MET cc_start: 0.9066 (mmm) cc_final: 0.8695 (mmm) REVERT: J 176 GLN cc_start: 0.9231 (mm110) cc_final: 0.8962 (mm110) REVERT: J 230 LEU cc_start: 0.9367 (tp) cc_final: 0.9115 (mm) REVERT: J 254 GLU cc_start: 0.3765 (mm-30) cc_final: 0.3506 (mm-30) REVERT: J 357 TYR cc_start: 0.8986 (m-80) cc_final: 0.8567 (m-80) REVERT: J 411 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7889 (mm-30) REVERT: J 432 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7117 (t80) REVERT: H 55 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7514 (tm-30) REVERT: H 76 ASP cc_start: 0.8916 (m-30) cc_final: 0.8377 (m-30) REVERT: H 110 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8484 (mm-30) REVERT: H 160 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8221 (tp30) REVERT: H 183 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7927 (mt-10) REVERT: H 205 ASP cc_start: 0.8645 (t0) cc_final: 0.8343 (t0) REVERT: H 211 ASP cc_start: 0.9114 (m-30) cc_final: 0.8832 (t70) REVERT: H 215 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7122 (mtp180) REVERT: H 352 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8494 (tttp) REVERT: H 420 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8776 (mm-30) REVERT: H 431 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8064 (mm-30) REVERT: L 47 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6251 (m-30) REVERT: L 76 ASP cc_start: 0.8970 (m-30) cc_final: 0.8611 (m-30) REVERT: L 112 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8503 (ptpp) REVERT: L 113 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8204 (mp0) REVERT: L 120 ASP cc_start: 0.9085 (t0) cc_final: 0.8868 (t0) REVERT: L 199 ASP cc_start: 0.8978 (m-30) cc_final: 0.8522 (m-30) REVERT: L 259 LEU cc_start: 0.9384 (tt) cc_final: 0.8915 (mt) REVERT: L 269 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8880 (pp) REVERT: L 411 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8212 (mm-30) REVERT: L 415 GLU cc_start: 0.8427 (pm20) cc_final: 0.7904 (mt-10) REVERT: L 430 LYS cc_start: 0.9263 (tppt) cc_final: 0.9021 (tppt) REVERT: L 433 GLU cc_start: 0.9189 (tp30) cc_final: 0.8800 (tp30) REVERT: G 1 MET cc_start: 0.9122 (mmm) cc_final: 0.8542 (mmp) REVERT: G 151 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8799 (m) REVERT: G 290 GLU cc_start: 0.8573 (tt0) cc_final: 0.8272 (tt0) REVERT: G 293 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8588 (pp30) REVERT: K 112 LYS cc_start: 0.8678 (pttm) cc_final: 0.8258 (pttm) REVERT: K 176 GLN cc_start: 0.9039 (mm110) cc_final: 0.8743 (mm110) REVERT: K 254 GLU cc_start: 0.4215 (mm-30) cc_final: 0.3871 (mm-30) REVERT: K 293 ASN cc_start: 0.9185 (m-40) cc_final: 0.8675 (m-40) REVERT: K 308 ARG cc_start: 0.9197 (mpp80) cc_final: 0.8939 (mpp80) REVERT: K 326 LYS cc_start: 0.6241 (mmtt) cc_final: 0.5318 (pttt) REVERT: K 339 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8433 (tpp-160) REVERT: K 342 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: K 357 TYR cc_start: 0.9063 (m-80) cc_final: 0.8601 (m-80) REVERT: K 411 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8014 (mm-30) REVERT: K 423 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8259 (mt-10) REVERT: I 12 CYS cc_start: 0.8676 (t) cc_final: 0.8110 (t) REVERT: I 47 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8185 (mm-30) REVERT: I 59 ASN cc_start: 0.8695 (m-40) cc_final: 0.8307 (p0) REVERT: I 71 GLU cc_start: 0.8394 (tp30) cc_final: 0.8069 (tm-30) REVERT: I 205 ASP cc_start: 0.8472 (t0) cc_final: 0.8121 (t0) REVERT: I 211 ASP cc_start: 0.8995 (m-30) cc_final: 0.8396 (t0) REVERT: I 215 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.7925 (mtm-85) REVERT: I 309 HIS cc_start: 0.9339 (m90) cc_final: 0.8975 (m90) REVERT: I 386 GLU cc_start: 0.8664 (pt0) cc_final: 0.8313 (pt0) REVERT: I 405 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8983 (tt) REVERT: P 338 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7384 (t) outliers start: 122 outliers final: 97 residues processed: 1003 average time/residue: 0.2349 time to fit residues: 392.7106 Evaluate side-chains 1030 residues out of total 4450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 917 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain T residue 303 ILE Chi-restraints excluded: chain T residue 307 PHE Chi-restraints excluded: chain T residue 325 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 295 MET Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 203 MET Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 192 HIS Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 255 PHE Chi-restraints excluded: chain K residue 342 GLN Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 37 HIS Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 295 MET Chi-restraints excluded: chain I residue 405 LEU Chi-restraints excluded: chain P residue 307 PHE Chi-restraints excluded: chain P residue 338 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 190 optimal weight: 7.9990 chunk 202 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 445 optimal weight: 0.0470 chunk 417 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 489 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN B 281 GLN B 293 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 311 GLN F 281 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN ** H 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN K 342 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 349 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075887 restraints weight = 72756.039| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.12 r_work: 0.2965 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 42070 Z= 0.205 Angle : 0.747 59.200 57162 Z= 0.418 Chirality : 0.052 1.852 6252 Planarity : 0.006 0.231 7436 Dihedral : 9.468 155.978 5764 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.86 % Allowed : 21.18 % Favored : 75.96 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 5160 helix: 1.74 (0.10), residues: 2452 sheet: 1.02 (0.19), residues: 786 loop : -0.57 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 278 TYR 0.092 0.001 TYR B 185 PHE 0.032 0.001 PHE D 20 TRP 0.025 0.002 TRP H 346 HIS 0.334 0.004 HIS K 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (42070) covalent geometry : angle 0.74685 / 0.42 (57162) hydrogen bonds : bond 0.04601 / 3.11 ( 2119) hydrogen bonds : angle 4.54229 / 3.28 ( 6123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10933.94 seconds wall clock time: 188 minutes 4.01 seconds (11284.01 seconds total)